All Gene Supplementary Material - Additional samples removed.

Load Libraries

# libraries used for analysis
library(edgeR)
library(limma)
library(quadprog)
library(ruv)

# libraries required for graphics
library(ggplot2)
library(reshape2)
library(EDASeq)
library(RColorBrewer)
library(VennDiagram)
library(data.table)
library(dplyr)
library(stringr)
library(knitr)
library(pheatmap)


wd = "./"
colors <- c("#0571b0", "#ca0020")

Load our data

We first produce a matrix of read counts after aligning to both the Human and Plasmodium falciparum 3D7 reference genome. Subread’s featureCounts program is then used to allocate reads to gene features using the gff file PlasmoDB-12.0_Pfalciparum3D7.gff from PlasmoDB. For both Subread programs the default options are used.

setwd(wd)
# # Next subreads featureCounts was used to allocate reads to genes. This
# was saved for re-use files <-
# Sys.glob('/home/users/allstaff/tonkin-hill.g/all_gene_analysis/alignment/*.sam')
# fc_genes_aligned_w_Pfhuman_withoutVivax <- featureCounts(files, annot.ext
# = './data/PlasmoDB-12.0_Pfalciparum3D7.gff' , isPairedEnd=TRUE,
# isGTFAnnotationFile=TRUE, GTF.attrType='ID', GTF.featureType='gene' ,
# nthreads=15)

# Load gene ID mappings which we use later on.
geneID_mappings <- fread("./data/geneID_mappings.txt", data.table = FALSE, stringsAsFactors = FALSE)
trim <- function(x) gsub("^\\s+|\\s+$", "", x)
s <- str_split(as.character(geneID_mappings$`[Previous ID(s)]`), ",")
geneID_mappings <- data.frame(current = rep(geneID_mappings$`[Gene ID]`, sapply(s, 
    FUN = length)), old = unlist(s))
geneID_mappings$old <- str_trim(geneID_mappings$old)

# Load read counts (if featureCounts has been run previously)
load("./data/fc_genes_with_all_samples_aligned_human_Pf_WithOutVivax_subread_uH.RData")
fc2 <- fc_genes_aligned_w_Pfhuman_withoutVivax
t <- fc2$counts

# Rename samples to something more sensible colnames(t) <-
# gsub('alignment\\.sam','',colnames(t)) colnames(t) <-
# gsub('.*vivax\\.','',colnames(t)) colnames(t) <- gsub('_S.*','',
# colnames(t))
fc2$counts <- t

x <- DGEList(counts = fc2$counts, genes = fc2$annotation)

Initial filter

We next filter out genes that do not have sufficient coverage across our samples for reliable estimates to be made.

setwd(wd)
before <- nrow(x$counts)
keep <- rowSums(cpm(x) > 2) >= 10
x <- x[keep, , keep.lib.sizes = FALSE]

We require that there are at least 2 reads per million for at least 10 samples in order for a gene to be included in the analysis. This reduced the number of genes being considered from 5777 to 4144.

Remove low depth samples

setwd(wd)
bplot <- melt(colSums(x$counts))
colnames(bplot) <- c("Read.Counts")
bplot$Sample <- rownames(bplot)

gg <- ggplot(bplot, aes(x = factor(Sample), y = Read.Counts)) + geom_bar(stat = "identity")
gg <- gg + theme_bw() + scale_y_sqrt(breaks = c(0, 10000, 1e+06, 1e+07, 1e+08))
gg <- gg + theme(axis.text.x = element_text(size = 12, angle = 90), axis.text.y = element_text(size = 12, 
    angle = 0), axis.title = element_text(size = 14, face = "bold"))
gg <- gg + labs(x = "Sample", y = "Read Count")
gg <- gg + geom_hline(aes(yintercept = 1e+06), col = "red")

x$counts <- x$counts[, !grepl("SFD1|SFM9|SFC\\.025", colnames(x$counts))]
filt.annnotation <- fc2$annotation[fc2$annotation$GeneID %in% rownames(x$counts), 
    ]
dge <- DGEList(counts = x$counts, genes = filt.annnotation)

gg

Samples SFD1, SFM9 and SFC.025 were not sequenced to a sufficient depth to be reliable and thus are removed.

Remove drug treated samples

Samples SFU2 and SFU3 were drug treated and are removed. We repeated the analysis of the all gene DGE omitting a few patients who had anti-malarial treatments in preceding months. The patients omitted are: SFC 023, SFM007, IFM 012 and IFM 021.

x$counts <- x$counts[, !grepl("SFU2|SFU\\.3", colnames(x$counts))]
x$counts <- x$counts[, !grepl("SFC\\.023|SFM\\.7|IFM12|IFM21", colnames(x$counts))]
filt.annnotation <- fc2$annotation[fc2$annotation$GeneID %in% rownames(x$counts), 
    ]
dge <- DGEList(counts = x$counts, genes = filt.annnotation)

Now we take the log transform of our sample counts (RPKM) to estimate the proportion of different stages present.

setwd(wd)
our_log_rpkm <- rpkm(dge)
our_log_rpkm <- log2(1 + our_log_rpkm)

Estimate Contributions from Different Life-cycle Stages

Load Data

To estimate the proportion of different life-cycle stages in each of our samples we require a reference data set. Su et al provide such a reference. They performed RNA-seq at two gametocyte stages, an ookinete stage and four time points of erythrocytic stages representing ring, early trophozoite, late trophozoite, and schizont. As we do not expect any ookinete stage parasites we discarded this reference. The data was downloaded from PlasmoDB and as such read counts were reported in RPKM. To handle outlying counts in a sensible manner a log2 transformation of the RPKM values was performed. This was also done for our gene counts. By next fitting a mixture model we can estimate the proportion of different parasite stages that make up our samples.

setwd(wd)
su_rpkm <- read.csv("./data/ rpkm_7SexualAndAsexualLifeStages_suetal.csv", header = TRUE, 
    sep = ",")

# ignore the Ookinete profile as this should be absent from our data.
su_rpkm$Ookinete <- NULL
rownames(su_rpkm) <- su_rpkm$ID
su_rpkm$ID <- NULL

# take the log transform of the data which helps to manage outlier genes.
su_log_rpkm <- log2(1 + su_rpkm)

Mixture Model

Given a set of stages \(S\) and a set of genes \(g_i: i\in \{1,...,N\}\) we want to minimise

\[ \sum_{i=1}^N \left( g_{i,sample} - \sum_{s \in S} \pi_s g_{i,s} \right)^2 \]

Subject to constraints

\[ \sum_{s\in S} \pi_s = 1 \]

\[ \pi_s > 0 \]

Here \(\pi_s\) is proportion of stage \(s\) that is attributed to having contributed to our sample. This model was fit using R’s solve.QP function.

setwd(wd)
findMix <- function(Y, X) {
    X[is.na(X)] <- t(replicate(ncol(X), apply(X, 1, mean, na.rm = T)))[is.na(X)]
    Rinv <- solve(chol(t(X) %*% X))
    C <- cbind(rep(1, ncol(X)), diag(ncol(X)))
    b <- c(1, rep(0, ncol(X)))
    d <- t(Y) %*% X
    qp <- solve.QP(Dmat = Rinv, factorized = TRUE, dvec = d, Amat = C, bvec = b, 
        meq = 1)
    sol <- qp$solution
    sol[sol < 1e-10] <- 0
    return(sol)
}

Calculate Sample Life-Cycle Profiles

We fit this mixture model to each of our samples in turn. The results are then plotted. A column represents each sample in the plot below. As we are fitting proportion parameters each columns values must add to 1 over the 5 stages. Note that we have also combined the estimated proportions for the gametocyte samples into one gametocyte variable. The columns are coloured by phenotype.

setwd(wd)
# First get the intersection of the genes for the two datasets and order
# them by rowname.
inter <- intersect(rownames(our_log_rpkm), rownames(su_log_rpkm))

O <- our_log_rpkm[rownames(our_log_rpkm) %in% inter, ]
O <- O[order(rownames(O)), ]
S <- su_log_rpkm[rownames(su_log_rpkm) %in% inter, ]
S <- S[order(rownames(S)), ]

# Now lets fit some samples!
ourPlotData <- data.frame()
for (i in 1:ncol(O)) {
    mix <- findMix(O[, i], as.matrix(S))
    ourPlotData <- rbind(ourPlotData, data.frame(sample = rep(colnames(O)[i], 
        ncol(S)), stage = colnames(S), proportion = mix))
}

# Organise the results.
ourPlotData$stage <- gsub("Gametocyte.*", "Gametocyte", ourPlotData$stage)
ourPlotData <- aggregate(proportion ~ sample + stage, data = ourPlotData, FUN = sum)
ourPlotData <- within(ourPlotData, stage <- factor(stage, levels = c("Ring", 
    "Early.Trophozoite", "Late.Trophozoite", "Schizont", "Gametocyte")))
ourPlotData$phenotype <- ifelse(substring(ourPlotData$sample, 1, 1) == "I", 
    "non-severe", "severe")

# Make a pretty plot.
gg <- ggplot(ourPlotData, aes(x = factor(sample), y = proportion, fill = factor(phenotype))) + 
    geom_bar(stat = "identity")
gg <- gg + scale_fill_manual(values = c(`non-severe` = "#2c7bb6", severe = "#d7191c"))
gg <- gg + facet_wrap(~stage, ncol = 1)
gg <- gg + theme_bw()
gg <- gg + theme(axis.text.x = element_text(size = 12, angle = 90), axis.text.y = element_text(size = 12, 
    angle = 0), axis.title = element_text(size = 14, face = "bold"), strip.text.x = element_text(size = 16, 
    face = "bold"))
gg <- gg + labs(x = "Sample", y = "Proportion", fill = "Stage")
gg <- gg + theme(legend.text = element_text(size = 14))
gg <- gg + theme(legend.key.size = unit(0.25, "in"))
gg <- gg + theme(legend.title = element_text(size = 16, face = "bold"))
gg <- gg + guides(fill = guide_legend(title = "Phenotype"))
gg

Investigate Differential Expression

We now perform the Voom transformation on our count matrix. Prior to the transformation we use TMM normalisation to account for the different library sizes present in our sample. TMM was chosen as it is more robust to outliers. From the Voom variance trend it is evident that there are a number of genes that have both high variability and high expression. After looking at some of the main offenders these were identified to be influenced by staging in the parasite. Consequently it is important to account for life-cycle stage when conducting the differential expression analysis.

options(width = 150)
setwd(wd)
categories <- as.factor(substring(rownames(dge$samples), 1, 1))
dge <- calcNormFactors(dge, method = "TMM")
dge$samples$group <- categories
design <- model.matrix(~group, data = dge$samples)

v <- voom(dge, design = design, plot = TRUE)

PCA Normalising for Library Size

The PCA plot below indicates that accounting for library size alone does not cope with the impact of life-cycle stages. Notably SFC21 is clearly an outlier and was identified in the mixture model as containing later stage parasites as well as gametocytes. IFM14 is also slightly separate in the PCA plot and was identified as having a proportion of Schizont stage parasite present.

setwd(wd)
plotPCA(v$E, col = colors[categories], cex = 0.8, isLog = TRUE)

Further the Relative Log Expression (RLE) plot below suggests that there is something different about SFC21 as well as highlighting IFM060 as being different.

setwd(wd)
plotVoomRLE <- function(E, colours) {
    mn <- apply(E, 1, median)
    rle <- data.frame(sweep(E, MARGIN = 1, STATS = mn, FUN = "-"))
    boxplot(rle, col = colours, outline = FALSE, las = 2, ylim = c(-7, 7))
    abline(h = 0, col = "black")
}
plotVoomRLE(v$E, colors[categories])

PCA Normalising for Library Size, Ring, Gametocyte and Schizont effects.

To investigate the impact of life-cycle stages in our analysis we fit a linear model using limma’s removeBatchEffect. Initially ring, gametocyte and schizont parameters were fit along with the disease phenotype factor. This was because for the most part the Trophozoite stages could be represented by accounting for these stages as they would be present implicitly in the model.

The PCA indicates that we have dealt with the outlying SFC21 sample as well as other less outlying samples such as IFM14 which showed a proportion of Schizont stage parasites in the mixture model. Unfortunately due to the low number of samples that have proportions of Schizont and Gametocytes estimating differential differential expression in severe disease becomes impossible. This is because there is insufficient data to estimate these stage parameters and consequently the uncertainty in the model is too high to find significant differences between severe and non-severe disease.

setwd(wd)
covs <- data.frame(v$design[, 2])
ourPlotData$phenotype <- NULL
c <- dcast(ourPlotData, sample ~ ..., value.var = "proportion")
covs <- merge(covs, c, by.x = 0, by.y = "sample")

colnames(covs) <- c("sample", "disease", colnames(c)[2:ncol(c)])
rownames(covs) <- covs$sample
covs$sample <- NULL
covs <- covs[match(colnames(v$E), rownames(covs)), ]
stopifnot(colnames(v$E) == rownames(covs))
# head(covs)

covs <- covs[, c(1, 2, 5, 6)]
# head(covs)

mod = model.matrix(as.formula(paste("~", paste(colnames(covs), collapse = " + "), sep = "")), data = covs)

norm_counts_ring <- removeBatchEffect(v$E, covariates = mod[, 3:ncol(mod)], design = mod[, 1:2])
plotPCA(norm_counts_ring, col = colors[categories], cex = 0.8, isLog = TRUE)

The RLE plot also suggests we have dealt with SFC21 however accounting for these stages does not seem to have accounted for the differences we see in the IFM060 sample. The mixture model did not identify IFM060 as being noticeably different from the other samples and consequently it is likely that there is some other unknown factor impacting on its expression.

setwd(wd)
plotVoomRLE(norm_counts_ring, col = colors[categories])

PCA Normalising for Library Size and Ring Stage Effects

We then investigate the impact of only accounting for the Ring stage parameter in the model. This gives us more power with which to identify differential expression related to severe disease. However, from the PCA plot below it is clear that accounting for Ring stage alone is insufficient and fails to adequately deal with SFC21.

setwd(wd)
covs <- covs[, c(1, 2)]

mod = model.matrix(as.formula(paste("~", paste(colnames(covs), collapse = " + "), sep = "")), data = covs)

norm_counts_ring <- removeBatchEffect(v$E, covariates = mod[, 3:ncol(mod)], design = mod[, 1:2])
plotPCA(norm_counts_ring, col = colors[categories], cex = 0.8, isLog = TRUE)

We are however able to identify differentially expressed genes in this less parameterised model. The summary of results accounting only for the Ring stage variable are given below. This test was performed using the limma-Voom pipeline. Ideally we would be able to keep both the power in out tests and account for the remaining unwanted factors. To achieve this we make use of RUV-4 to estimate dummy variables that represent multiple unknown factors of unwanted variation.

setwd(wd)
stopifnot(colnames(dge) == rownames(mod))
v2 <- voom(dge, design = mod, plot = FALSE)
fit <- lmFit(v2, mod)
fit <- eBayes(fit, robust = TRUE)

summary(de1 <- decideTests(fit, adjust.method = "BH", p.value = 0.05))

##    (Intercept) disease Ring
## -1          81      18 1265
## 0          681    4069 1734
## 1         3382      57 1145

Estimate Unwanted Factors of Variation

To cope with the outlier samples such as SFC21 whilst retaining statistical power we estimate factors of unwanted variation using RUV-4.
RUV-4 requires a set of control genes which are believed to be relatively unaffected by the condition of interest, in our case this is disease severity. RUV-4 is however fairly robust to the choice of control genes.
We chose to use the 1000 genes found to have the highest p-values in the experiment of Vignali et al as controls. The experiment of Vignali et al looked at differences in expression between pregnancy associated malaria and childhood malaria. Although this is not the same association we are investigating it was considered close enough to perform adequately as a source of control genes. Further an analysis using SVA which does not require controls and rather estimates them empirically was found to produce similar results with only 5 out of 119 genes found using SVA missing from the RUV-4 approach. Further RUV-4 attempts to recover some variation that may be lost in the vanilla SVA approach when the factor of interest (severe disease) correlates with an unwanted factor. Consequently it leads to a higher number of differentially expressed genes being found. It was also thought that having an independently sourced set of control genes was preferable to empirically deriving such a set.

setwd(wd)
contol_genes_vignali <- read.table("./data/contol_genes_vignali.txt", quote = "\"")

ctrl_vignali <- geneID_mappings$current[geneID_mappings$old %in% contol_genes_vignali$V1]
length(ctrl_vignali)

## [1] 1009

empirical_controls <- ctrl_vignali[0:length(ctrl_vignali)]
empirical_controls <- rownames(v$E) %in% empirical_controls

categoriesRUV <- categories
categoriesRUV <- data.matrix(as.numeric(categoriesRUV == "S"))
ring <- data.matrix(mod[, c(1, 3)])
genes <- data.matrix(t(v$E))

ruv <- RUV4(genes, categoriesRUV, empirical_controls, 3, Z = ring)

modRUV = cbind(mod, ruv$W)

norm_counts_ring_ruv <- removeBatchEffect(v$E, covariates = modRUV[, 3:ncol(modRUV)], design = modRUV[, 1:2])

Note that although we used 1000 genes from the experiment of Vignali et al only 533 were found in our reduced expression matrix.

The PCA plot below indicates that we have dealt with most of the problems due to staging. Here we have included the Ring stage proportion from the mixture model as well as three factors of unwanted variation estimated using RUV-4.

setwd(wd)
plotPCA(norm_counts_ring_ruv, col = colors[categories], cex = 0.8, isLog = TRUE)

The RLE plot also indicates that we have succesfully dealt with most of the staging issues. Both SFC21 and IFM14 have reasonable box plots. Moreover, IFM060 has a nicer boxplot indicating that in using RUV-4, not only have we dealt with staging issues, we have also accounted for some other unknown confounding factors that would have impacted our results. The variation in each sample has also been reduced which is indicated in the reduced height of the boxplot whiskers. Finally, the results were found to be relatively robust to the removal of the outlier samples such as SFC21 and IFM14. Consequently, this approach seems to succesfully deal with both life-cycle staging issues and other unknown impacting factors.

setwd(wd)
plotVoomRLE(norm_counts_ring_ruv, colors[categories])

Identify DE Genes using Limma and Voom

We now use the limma-voom pipeline, with the robust ebayes option which handles dispersion outliers. This was done to further ensure our results were less likely to be affected by outlier samples. Multiple testing correction was performed using the Benjamini-Hochberg approach.

setwd(wd)
stopifnot(colnames(dge) == rownames(modRUV))
v2 <- voom(dge, design = modRUV, plot = F)
fit <- lmFit(v2, modRUV)
fit <- eBayes(fit, robust = TRUE)
s <- summary(de2 <- decideTests(fit, adjust.method = "BH", p.value = 0.05))
s

##    (Intercept) disease Ring               
## -1          91      72 1393 1621 1101  478
## 0          548    4033 1450 1651 2070 3114
## 1         3505      39 1301  872  973  552

Overall 111 genes were found to be differentially expressed between severe and non-severe cases of malaria with a false dicovery rate threshold of 0.05.

A good check for validity of our model it to look at the distribution of the resulting p-values. If everything is okay we would expect a uniform distribution except near \(p=0\) where we would hope to see a spike. The barplot below indicates this is what we see which is helpful in affirming that we have done okay in removing unwanted variation without negatively impacting on the variation due to the variable of interest (diseas severity).

setwd(wd)
top_ring_ruv <- topTable(fit, coef = 2, p.value = 0.1, sort.by = "p", number = Inf, adjust.method = "BH", confint = TRUE)
hist <- data.frame(topTable(fit, coef = 2, number = Inf))
gg <- ggplot(hist, aes(x = P.Value)) + geom_histogram(binwidth = 0.01)
gg <- gg + theme_bw()
gg <- gg + theme(axis.text.x = element_text(size = 12), axis.text.y = element_text(size = 12, angle = 0), axis.title = element_text(size = 12, face = "bold"))
gg <- gg + labs(x = "P value", y = "Count")
gg

Results table

Below is a table of genes that were found to be differentially expressed, ordered by their respective p-values. The 95% confidence intervals are given with the estimated LFC as well as the BH adjusted p-values and the log-odds that the gene is differentially expressed. Here we report for interest sake all genes up to a adjusted p-value threshold of 0.1.

setwd(wd)
# Load additional gene information
GeneAnnotationPlasmoDB <- fread("./data/GeneAnnotationPlasmoDB.txt", data.table = FALSE, na.strings = "N/A")

# First lets import some additional gene information to make a nicer table
GeneAnnotationPlasmoDB <- GeneAnnotationPlasmoDB[, colnames(GeneAnnotationPlasmoDB) %in% c("[Gene ID]", "[Product Description]", "[Gene Name or Symbol]")]
top_ring_ruv <- merge(top_ring_ruv, GeneAnnotationPlasmoDB, by.x = 0, by.y = "[Gene ID]", all.x = TRUE)
top_ring_ruv <- top_ring_ruv[with(top_ring_ruv, order(adj.P.Val)), ]

# Now print the table
top_ring_ruv$P.Value <- format(top_ring_ruv$P.Value, scientific = TRUE, digits = 3)
top_ring_ruv$adj.P.Val <- format(top_ring_ruv$adj.P.Val, scientific = TRUE, digits = 3)
kable(top_ring_ruv[, c(2:4, 6:ncol(top_ring_ruv))], digits = 3)

	GeneID	Chr	Start	Strand	Length	logFC	CI.L	CI.R	AveExpr	t	P.Value	adj.P.Val	B	[Product Description]	[Gene Name or Symbol]
9	PF3D7_0115700	Pf3D7_01_v3	607390	-	7504	-1.695	-2.671	-0.718	4.472	-5.551	2.64e-06	5.48e-03	4.604	erythrocyte membrane protein 1, PfEMP1	VAR
14	PF3D7_0202000	Pf3D7_02_v3	103385	-	2412	-2.232	-3.132	-1.331	14.042	-5.745	2.34e-06	5.48e-03	4.796	knob-associated histidine-rich protein	KAHRP
271	PF3D7_1255200	Pf3D7_12_v3	2241271	-	7692	-1.490	-2.030	-0.951	4.566	-5.412	4.07e-06	5.63e-03	4.217	erythrocyte membrane protein 1, PfEMP1	VAR
23	PF3D7_0223500	Pf3D7_02_v3	916352	-	7297	-1.139	-1.932	-0.345	5.205	-4.963	1.63e-05	8.42e-03	2.967	erythrocyte membrane protein 1, PfEMP1	VAR
31	PF3D7_0316600	Pf3D7_03_v3	669302	-	1572	-1.407	-1.944	-0.870	10.248	-5.170	9.43e-06	8.42e-03	3.437	formate-nitrite transporter	FNT
37	PF3D7_0400100	Pf3D7_04_v3	28706	+	8972	-1.593	-1.921	-1.266	4.810	-5.026	1.34e-05	8.42e-03	3.137	erythrocyte membrane protein 1, PfEMP1	VAR
156	PF3D7_0900100	Pf3D7_09_v3	20080	+	7806	-1.462	-2.010	-0.915	4.673	-5.057	1.22e-05	8.42e-03	3.222	erythrocyte membrane protein 1, PfEMP1	VAR
189	PF3D7_1023600	Pf3D7_10_v3	987358	-	2791	-2.045	-3.030	-1.060	-0.122	-4.980	1.54e-05	8.42e-03	2.470	conserved Plasmodium protein, unknown function	NA
243	PF3D7_1223900	Pf3D7_12_v3	972710	-	684	-2.228	-4.701	0.246	2.658	-4.936	1.86e-05	8.58e-03	2.759	50S ribosomal protein L24, putative	NA
142	PF3D7_0809100	Pf3D7_08_v3	459312	+	7256	-1.773	-3.635	0.089	3.226	-4.884	2.08e-05	8.60e-03	2.660	erythrocyte membrane protein 1, PfEMP1	VAR
4	PF3D7_0106000	Pf3D7_01_v3	255775	-	2769	1.185	0.199	2.172	1.476	4.664	4.07e-05	1.23e-02	1.911	conserved Plasmodium protein, unknown function	NA
36	PF3D7_0324900	Pf3D7_03_v3	1030822	-	7433	-1.274	-2.295	-0.254	3.988	-4.507	6.54e-05	1.23e-02	1.679	erythrocyte membrane protein 1, PfEMP1	VAR
40	PF3D7_0404600	Pf3D7_04_v3	247731	+	12417	-1.457	-1.770	-1.145	7.604	-4.502	7.43e-05	1.23e-02	1.518	conserved Plasmodium membrane protein, unknown function	NA
45	PF3D7_0412700	Pf3D7_04_v3	561667	-	7676	-1.440	-2.188	-0.692	4.841	-4.530	6.09e-05	1.23e-02	1.754	erythrocyte membrane protein 1, PfEMP1	VAR
85	PF3D7_0600600	Pf3D7_06_v3	29618	-	1867	-1.681	-2.462	-0.901	3.049	-4.700	3.63e-05	1.23e-02	2.150	erythrocyte membrane protein 1 (PfEMP1), exon 2	VAR
105	PF3D7_0632800	Pf3D7_06_v3	1374797	-	7831	-1.240	-1.577	-0.904	4.681	-4.544	5.85e-05	1.23e-02	1.791	erythrocyte membrane protein 1, PfEMP1	VAR
107	PF3D7_0703100	Pf3D7_07_v3	121414	+	543	0.985	0.194	1.777	3.582	4.477	7.15e-05	1.23e-02	1.585	conserved Plasmodium protein, unknown function	NA
120	PF3D7_0712600	Pf3D7_07_v3	566726	-	7583	-1.748	-2.417	-1.079	3.429	-4.685	3.80e-05	1.23e-02	2.140	erythrocyte membrane protein 1, PfEMP1	VAR
133	PF3D7_0800100	Pf3D7_08_v3	21361	+	7293	-1.596	-2.257	-0.936	4.508	-4.513	6.58e-05	1.23e-02	1.687	erythrocyte membrane protein 1, PfEMP1	VAR
136	PF3D7_0802000	Pf3D7_08_v3	146089	+	4194	-1.266	-1.753	-0.778	9.188	-4.509	6.90e-05	1.23e-02	1.563	glutamate dehydrogenase, putative	GDH3
175	PF3D7_1000100	Pf3D7_10_v3	28490	+	7675	-1.339	-1.639	-1.040	4.505	-4.569	5.41e-05	1.23e-02	1.861	erythrocyte membrane protein 1, PfEMP1	VAR
204	PF3D7_1105100	Pf3D7_11_v3	226065	+	354	-1.063	-1.589	-0.536	9.705	-4.600	5.10e-05	1.23e-02	1.803	histone H2B	H2B
216	PF3D7_1123100	Pf3D7_11_v3	909366	+	6959	-0.597	-0.908	-0.287	9.103	-4.524	6.21e-05	1.23e-02	1.615	calcium-dependent protein kinase 7	CDPK7
231	PF3D7_1200100	Pf3D7_12_v3	16973	+	7525	-1.592	-2.227	-0.957	4.052	-4.609	4.80e-05	1.23e-02	1.962	erythrocyte membrane protein 1, PfEMP1	VAR
296	PF3D7_1344800	Pf3D7_13_v3	1796274	+	1436	-0.768	-1.123	-0.413	6.260	-4.560	5.58e-05	1.23e-02	1.805	aspartate carbamoyltransferase	ATCase
248	PF3D7_1228800	Pf3D7_12_v3	1169557	-	9630	-0.657	-1.727	0.414	6.788	-4.415	8.63e-05	1.38e-02	1.368	WD repeat-containing protein, putative	NA
84	PF3D7_0532400	Pf3D7_05_v3	1312471	+	1684	-1.315	-1.774	-0.856	8.118	-4.393	9.77e-05	1.40e-02	1.255	lysine-rich membrane-associated PHISTb protein	LyMP
102	PF3D7_0626200	Pf3D7_06_v3	1058666	-	1257	1.643	0.966	2.319	2.878	4.387	9.37e-05	1.40e-02	1.317	conserved Plasmodium protein, unknown function	NA
244	PF3D7_1224000	Pf3D7_12_v3	974372	+	1170	-1.670	-3.718	0.378	2.666	-4.378	9.63e-05	1.40e-02	1.295	GTP cyclohydrolase I	GCH1
322	PF3D7_1414200	Pf3D7_14_v3	564024	-	1224	0.818	0.286	1.349	5.924	4.353	1.04e-04	1.43e-02	1.236	conserved Plasmodium protein, unknown function	NA
198	PF3D7_1100100	Pf3D7_11_v3	24160	+	7439	-1.288	-1.828	-0.748	4.713	-4.310	1.18e-04	1.58e-02	1.149	erythrocyte membrane protein 1, PfEMP1	VAR
6	PF3D7_0109700	Pf3D7_01_v3	379149	-	658	-1.423	-2.847	0.001	4.127	-4.269	1.33e-04	1.73e-02	1.039	rRNA biogenesis protein RRP36, putative	RRP36
71	PF3D7_0519500	Pf3D7_05_v3	801450	-	7678	-0.942	-1.573	-0.311	7.017	-4.157	1.86e-04	2.09e-02	0.644	carbon catabolite repressor protein 4, putative	CCR4
153	PF3D7_0830300	Pf3D7_08_v3	1290240	-	1167	1.591	1.299	1.884	2.023	4.162	1.83e-04	2.09e-02	0.689	sporozoite invasion-associated protein 2	SIAP2
168	PF3D7_0925300	Pf3D7_09_v3	1019164	-	1740	2.109	1.367	2.850	0.173	4.158	1.86e-04	2.09e-02	0.526	proline–tRNA ligase, putative	aPRS
193	PF3D7_1028000	Pf3D7_10_v3	1160031	+	3391	-0.991	-1.656	-0.326	6.363	-4.158	1.86e-04	2.09e-02	0.671	methyltransferase, putative	NA
285	PF3D7_1316600	Pf3D7_13_v3	691014	+	3112	-1.262	-1.567	-0.958	6.456	-4.192	1.76e-04	2.09e-02	0.730	choline-phosphate cytidylyltransferase	CCT
117	PF3D7_0711700	Pf3D7_07_v3	511950	-	7476	-1.151	-1.908	-0.394	4.402	-4.081	2.34e-04	2.50e-02	0.535	erythrocyte membrane protein 1, PfEMP1	VAR
287	PF3D7_1318300	Pf3D7_13_v3	753910	+	5523	-1.051	-1.390	-0.712	5.766	-4.078	2.36e-04	2.50e-02	0.479	conserved Plasmodium protein, unknown function	NA
166	PF3D7_0917800	Pf3D7_09_v3	734629	+	1314	1.808	1.549	2.068	1.383	4.051	2.55e-04	2.64e-02	0.373	conserved Plasmodium protein, unknown function	NA
58	PF3D7_0500100	Pf3D7_05_v3	20929	+	7528	-1.287	-1.826	-0.748	3.399	-4.023	2.77e-04	2.68e-02	0.383	erythrocyte membrane protein 1, PfEMP1	VAR
224	PF3D7_1135300	Pf3D7_11_v3	1381015	-	1230	1.219	0.684	1.754	2.281	4.032	2.70e-04	2.68e-02	0.377	conserved Plasmodium membrane protein, unknown function	NA
238	PF3D7_1213100	Pf3D7_12_v3	576417	-	164	-2.305	-2.853	-1.757	2.312	-4.036	2.79e-04	2.68e-02	0.335	U1 spliceosomal RNA	NA
286	PF3D7_1316900	Pf3D7_13_v3	701047	-	2877	0.669	0.039	1.299	7.752	4.007	2.90e-04	2.73e-02	0.190	conserved Plasmodium protein, unknown function	NA
242	PF3D7_1223400	Pf3D7_12_v3	941125	+	5621	-0.766	-2.537	1.005	11.206	-3.995	3.01e-04	2.77e-02	0.107	phospholipid-transporting ATPase, putative	NA
124	PF3D7_0713600	Pf3D7_07_v3	617933	+	2935	1.165	0.776	1.554	3.264	3.969	3.24e-04	2.92e-02	0.244	mitochondrial ribosomal protein S5 precursor, putative	NA
41	PF3D7_0404900	Pf3D7_04_v3	267244	-	1137	1.903	1.310	2.495	3.340	3.976	3.31e-04	2.92e-02	0.230	6-cysteine protein	P41
65	PF3D7_0509000	Pf3D7_05_v3	376855	-	1598	-0.641	-1.129	-0.152	5.782	-3.938	3.55e-04	2.94e-02	0.097	SNAP protein (soluble N-ethylmaleimide-sensitive factor attachment protein), putative	NA
143	PF3D7_0810800	Pf3D7_08_v3	548200	+	2417	-1.107	-1.926	-0.288	7.387	-3.954	3.49e-04	2.94e-02	0.068	hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase	PPPK-DHPS
275	PF3D7_1303000	Pf3D7_13_v3	158144	+	635	-1.133	-2.435	0.170	3.355	-3.939	3.54e-04	2.94e-02	0.170	conserved Plasmodium protein, unknown function	NA
139	PF3D7_0805600	Pf3D7_08_v3	312034	+	927	0.774	0.335	1.213	7.188	3.895	4.02e-04	3.22e-02	-0.092	PAP2-like protein, putative	NA
315	PF3D7_1400100	Pf3D7_14_v3	1393	+	3951	-1.321	-1.729	-0.913	4.966	-3.901	4.04e-04	3.22e-02	0.024	erythrocyte membrane protein 1 (PfEMP1), pseudogene	NA
251	PF3D7_1230500	Pf3D7_12_v3	1253973	-	1509	0.909	-0.278	2.097	4.436	3.879	4.22e-04	3.30e-02	0.000	WD repeat-containing protein, putative	NA
24	PF3D7_0300100	Pf3D7_03_v3	36965	+	7518	-1.134	-1.505	-0.762	4.351	-3.865	4.39e-04	3.32e-02	-0.033	erythrocyte membrane protein 1, PfEMP1	VAR
265	PF3D7_1246600	Pf3D7_12_v3	1936522	+	1173	-0.852	-1.815	0.111	5.347	-3.864	4.40e-04	3.32e-02	-0.075	pre-mRNA-splicing factor CWC26, putative	BUD13
7	PF3D7_0113000	Pf3D7_01_v3	487892	-	2236	-1.480	-3.080	0.121	11.345	-3.858	5.27e-04	3.64e-02	-0.381	glutamic acid-rich protein	GARP
237	PF3D7_1212800	Pf3D7_12_v3	565966	+	966	1.021	0.421	1.621	2.457	3.805	5.22e-04	3.64e-02	-0.186	iron-sulfur subunit of succinate dehydrogenase	NA
260	PF3D7_1240900	Pf3D7_12_v3	1735543	+	7866	-1.406	-2.440	-0.371	4.296	-3.816	5.12e-04	3.64e-02	-0.163	erythrocyte membrane protein 1, PfEMP1	VAR
267	PF3D7_1249000	Pf3D7_12_v3	2005175	-	2019	1.002	0.352	1.652	1.154	3.821	4.98e-04	3.64e-02	-0.193	conserved Plasmodium membrane protein, unknown function	NA
347	PF3D7_1457000	Pf3D7_14_v3	2336649	-	2505	-0.648	-1.396	0.101	8.961	-3.813	5.11e-04	3.64e-02	-0.368	signal peptide peptidase	SPP
83	PF3D7_0532300	Pf3D7_05_v3	1308278	+	1663	-1.199	-1.939	-0.459	10.800	-3.818	5.46e-04	3.65e-02	-0.411	Plasmodium exported protein (PHISTb), unknown function	NA
316	PF3D7_1401400	Pf3D7_14_v3	53411	-	324	-0.853	-1.218	-0.488	12.466	-3.797	5.42e-04	3.65e-02	-0.439	early transcribed membrane protein 14.1	ETRAMP14
111	PF3D7_0704600	Pf3D7_07_v3	216024	-	13049	-0.663	-1.466	0.140	10.228	-3.766	5.84e-04	3.78e-02	-0.518	E3 ubiquitin-protein ligase	UT
205	PF3D7_1105300	Pf3D7_11_v3	231847	-	2392	1.352	1.003	1.700	1.696	3.767	5.82e-04	3.78e-02	-0.302	conserved Plasmodium protein, unknown function	NA
211	PF3D7_1118400	Pf3D7_11_v3	699869	-	921	1.065	0.445	1.685	3.280	3.756	6.02e-04	3.84e-02	-0.298	haloacid dehalogenase-like hydrolase, putative	NA
262	PF3D7_1244200	Pf3D7_12_v3	1852844	-	2838	1.031	0.729	1.333	5.481	3.739	6.32e-04	3.97e-02	-0.416	RNA polymerase II transcription factor B subunit 2, putative	TFB2
54	PF3D7_0419800	Pf3D7_04_v3	874811	-	711	0.644	0.109	1.179	5.924	3.733	6.43e-04	3.98e-02	-0.456	60S ribosomal protein L7ae/L30e, putative	NA
13	PF3D7_0201900	Pf3D7_02_v3	91318	-	7521	-1.527	-2.211	-0.843	10.614	-3.763	6.87e-04	4.12e-02	-0.606	erythrocyte membrane protein 3	EMP3
146	PF3D7_0821500	Pf3D7_08_v3	967901	-	840	0.820	0.569	1.070	4.918	3.706	6.94e-04	4.12e-02	-0.467	ribosomal RNA small subunit methyltransferase NEP1, putative	NEP1
147	PF3D7_0822200	Pf3D7_08_v3	982570	+	5127	1.108	0.550	1.666	2.942	3.700	7.07e-04	4.12e-02	-0.439	conserved Plasmodium membrane protein, unknown function	NA
149	PF3D7_0823800	Pf3D7_08_v3	1043813	+	1968	-0.753	-1.486	-0.020	5.245	-3.700	7.05e-04	4.12e-02	-0.514	DnaJ protein, putative	NA
51	PF3D7_0417400	Pf3D7_04_v3	756294	+	20310	-0.792	-1.152	-0.432	8.067	-3.685	7.37e-04	4.24e-02	-0.697	conserved Plasmodium protein, unknown function	NA
121	PF3D7_0712800	Pf3D7_07_v3	581386	-	7538	-1.348	-2.079	-0.616	4.007	-3.677	7.57e-04	4.24e-02	-0.507	erythrocyte membrane protein 1, PfEMP1	VAR
154	PF3D7_0831700	Pf3D7_08_v3	1365467	-	2040	-0.982	-1.261	-0.702	13.434	-3.690	7.53e-04	4.24e-02	-0.736	heat shock protein 70	HSP70-x
1	mal_rna_11:rRNA	M76611	1916	-	108	-1.640	-2.203	-1.077	1.870	-3.641	8.35e-04	4.27e-02	-0.608	NA	NA
25	PF3D7_0302800	Pf3D7_03_v3	148046	-	1260	1.163	0.554	1.772	5.270	3.630	8.76e-04	4.27e-02	-0.696	conserved Plasmodium protein, unknown function	NA
47	PF3D7_0413900	Pf3D7_04_v3	623168	-	3059	-0.742	-1.627	0.143	6.964	-3.656	8.01e-04	4.27e-02	-0.731	ubiquitin carboxyl-terminal hydrolase 13, putative	USP13
57	PF3D7_0423800	Pf3D7_04_v3	1076347	+	1188	2.290	1.835	2.746	2.134	3.628	9.24e-04	4.27e-02	-0.671	cysteine-rich protective antigen	CyRPA
68	PF3D7_0512000	Pf3D7_05_v3	527639	+	1028	-1.030	-1.691	-0.369	5.218	-3.609	9.15e-04	4.27e-02	-0.737	prefoldin subunit 6, putative	NA
81	PF3D7_0529000	Pf3D7_05_v3	1186787	-	2160	0.470	-0.311	1.252	7.651	3.631	8.60e-04	4.27e-02	-0.825	conserved Plasmodium protein, unknown function	NA
103	PF3D7_0629600	Pf3D7_06_v3	1218307	+	945	0.546	0.103	0.988	4.979	3.605	9.25e-04	4.27e-02	-0.730	conserved Plasmodium protein, unknown function	NA
116	PF3D7_0711200	Pf3D7_07_v3	495238	+	3003	1.222	0.659	1.785	2.256	3.636	8.47e-04	4.27e-02	-0.605	conserved Plasmodium protein, unknown function	NA
132	PF3D7_0733000	Pf3D7_07_v3	1417588	-	8647	-1.043	-1.615	-0.471	4.926	-3.623	8.79e-04	4.27e-02	-0.683	erythrocyte membrane protein 1, PfEMP1	VAR
161	PF3D7_0909600	Pf3D7_09_v3	433238	-	2136	1.511	1.178	1.843	0.836	3.642	8.34e-04	4.27e-02	-0.639	conserved Plasmodium protein, unknown function	NA
197	PF3D7_1041300	Pf3D7_10_v3	1642401	-	7548	-1.101	-1.727	-0.474	4.981	-3.628	8.68e-04	4.27e-02	-0.670	erythrocyte membrane protein 1, PfEMP1	VAR
213	PF3D7_1121100	Pf3D7_11_v3	794254	-	5308	-0.793	-1.429	-0.157	8.461	-3.604	9.27e-04	4.27e-02	-0.908	conserved Plasmodium protein, unknown function	NA
298	PF3D7_1346200	Pf3D7_13_v3	1845878	-	507	2.002	1.693	2.312	0.978	3.614	9.19e-04	4.27e-02	-0.704	nuclear import protein MOG1, putative	NA
326	PF3D7_1421150	Pf3D7_14_v3	875173	-	149	-1.649	-2.239	-1.059	1.022	-3.645	8.26e-04	4.27e-02	-0.630	C/D small nucleolar RNA	NA
337	PF3D7_1444800	Pf3D7_14_v3	1844041	-	1577	-0.692	-1.263	-0.122	10.290	-3.622	8.81e-04	4.27e-02	-0.895	fructose-bisphosphate aldolase	FBPA
346	PF3D7_1451800	Pf3D7_14_v3	2123461	+	3139	-0.690	-1.189	-0.190	4.615	-3.616	8.96e-04	4.27e-02	-0.698	sortilin	NA
207	PF3D7_1108700	Pf3D7_11_v3	373238	-	1623	0.745	0.222	1.267	6.854	3.584	9.81e-04	4.47e-02	-0.899	heat shock protein DnaJ homologue Pfj2	NA
95	PF3D7_0617200	Pf3D7_06_v3	717050	+	1868	-1.064	-2.315	0.188	7.853	-3.587	1.03e-03	4.57e-02	-0.986	conserved Plasmodium protein, unknown function	NA
299	PF3D7_1346400	Pf3D7_13_v3	1852898	+	17967	-0.706	-0.963	-0.449	7.849	-3.569	1.02e-03	4.57e-02	-0.999	conserved Plasmodium protein, unknown function	NA
259	PF3D7_1240600	Pf3D7_12_v3	1719574	+	7883	-1.224	-1.818	-0.629	3.851	-3.554	1.07e-03	4.66e-02	-0.812	erythrocyte membrane protein 1, PfEMP1	VAR
303	PF3D7_1354300	Pf3D7_13_v3	2164239	-	3178	-0.517	-1.135	0.102	9.432	-3.556	1.06e-03	4.66e-02	-1.072	large subunit rRNA methyltransferase, putative	NA
220	PF3D7_1126300	Pf3D7_11_v3	1026976	+	2569	1.067	0.818	1.316	4.596	3.543	1.10e-03	4.76e-02	-0.874	DnaJ protein, putative	NA
62	PF3D7_0503100	Pf3D7_05_v3	127064	-	1614	-1.336	-1.742	-0.929	2.177	-3.504	1.23e-03	4.80e-02	-0.920	4-diphosphocytidyl-2-C-methyl-D-erythritol kinase, putative	IspE
99	PF3D7_0622700	Pf3D7_06_v3	916000	-	1300	1.532	0.053	3.011	1.425	3.534	1.13e-03	4.80e-02	-0.860	conserved Plasmodium membrane protein, unknown function	NA
128	PF3D7_0719500	Pf3D7_07_v3	854652	-	2003	0.995	0.204	1.786	1.461	3.509	1.21e-03	4.80e-02	-0.923	LEM3/CDC50 family protein, putative	NA
170	PF3D7_0928500	Pf3D7_09_v3	1146239	-	959	-1.164	-2.209	-0.119	2.608	-3.509	1.21e-03	4.80e-02	-0.908	conserved Plasmodium protein, unknown function	NA
177	PF3D7_1003900	Pf3D7_10_v3	177921	+	950	1.677	0.884	2.470	0.332	3.524	1.16e-03	4.80e-02	-0.928	conserved Plasmodium protein, unknown function	NA
180	PF3D7_1012000	Pf3D7_10_v3	463493	+	3514	-0.679	-1.272	-0.085	6.052	-3.496	1.26e-03	4.80e-02	-1.086	E3 ubiquitin-protein ligase, putative	NA
202	PF3D7_1102800	Pf3D7_11_v3	131703	-	285	-0.910	-1.825	0.006	13.470	-3.540	1.15e-03	4.80e-02	-1.132	early transcribed membrane protein 11.2	ETRAMP11.2
288	PF3D7_1321600	Pf3D7_13_v3	897716	+	3329	1.398	0.495	2.301	0.132	3.515	1.19e-03	4.80e-02	-0.960	phosphodiesterase gamma, putative	PDEgamma
310	PF3D7_1365600	Pf3D7_13_v3	2621261	+	2740	0.733	-0.151	1.617	4.139	3.495	1.26e-03	4.80e-02	-0.965	DNA topoisomerase VI, b subunit, putative	NA
331	PF3D7_1428100	Pf3D7_14_v3	1098038	-	1914	0.966	0.460	1.473	3.882	3.497	1.26e-03	4.80e-02	-0.957	WW domain-binding protein 11, putative	NA
341	PF3D7_1446900	Pf3D7_14_v3	1924425	-	2226	0.763	0.448	1.079	6.864	3.500	1.24e-03	4.80e-02	-1.121	glutaminyl-peptide cyclotransferase, putative	NA
349	PF3D7_1457900	Pf3D7_14_v3	2375579	+	10368	-0.756	-1.417	-0.094	5.650	-3.528	1.15e-03	4.80e-02	-0.973	conserved Plasmodium protein, unknown function	NA
356	PF3D7_1470200	Pf3D7_14_v3	2877586	-	1163	-0.675	-1.356	0.006	5.398	-3.515	1.19e-03	4.80e-02	-0.979	conserved Plasmodium protein, unknown function	NA
138	PF3D7_0804900	Pf3D7_08_v3	279711	-	1476	0.919	-0.323	2.160	5.949	3.480	1.32e-03	4.96e-02	-1.111	GTPase-activating protein, putative	NA
338	PF3D7_1445600	Pf3D7_14_v3	1871778	+	2604	0.679	0.247	1.112	8.272	3.476	1.33e-03	4.97e-02	-1.254	RNA-binding protein, putative	NA
127	PF3D7_0717600	Pf3D7_07_v3	758720	-	4158	-1.473	-1.889	-1.056	3.059	-3.474	1.36e-03	5.02e-02	-1.007	conserved Plasmodium protein, unknown function	NA
73	PF3D7_0522300	Pf3D7_05_v3	902613	-	2232	-0.572	-1.174	0.030	6.700	-3.459	1.39e-03	5.09e-02	-1.221	S-adenosylmethionine-dependent methyltransferase, putative	NA
343	PF3D7_1449900	Pf3D7_14_v3	2044007	-	1023	1.308	0.758	1.858	2.638	3.457	1.40e-03	5.09e-02	-1.030	conserved Plasmodium protein, unknown function	NA
148	PF3D7_0823200	Pf3D7_08_v3	1022629	-	1218	-0.619	-0.974	-0.264	9.617	-3.453	1.42e-03	5.12e-02	-1.345	RNA-binding protein, putative	NA
335	PF3D7_1437800	Pf3D7_14_v3	1530276	-	555	1.770	1.086	2.453	2.830	3.457	1.44e-03	5.16e-02	-1.053	trafficking protein particle complex subunit 5, putative	TRAPPC5
28	PF3D7_0305000	Pf3D7_03_v3	234058	-	1277	0.947	0.074	1.820	3.438	3.441	1.47e-03	5.16e-02	-1.085	elongation factor Ts	EF-Ts
209	PF3D7_1111300	Pf3D7_11_v3	442959	-	870	0.841	0.548	1.135	2.945	3.438	1.48e-03	5.16e-02	-1.078	SNARE protein, putative	GS27
305	PF3D7_1355700	Pf3D7_13_v3	2206592	-	3867	1.237	0.365	2.109	7.278	3.465	1.48e-03	5.16e-02	-1.290	NLI interacting factor-like phosphatase, putative	NIF3
19	PF3D7_0216000	Pf3D7_02_v3	658636	+	5994	-2.074	-2.621	-1.528	0.535	-3.431	1.53e-03	5.29e-02	-1.144	DEAD/DEAH box helicase, putative	NA
53	PF3D7_0419500	Pf3D7_04_v3	866501	-	1611	1.223	0.163	2.283	3.890	3.421	1.55e-03	5.30e-02	-1.142	conserved Plasmodium membrane protein, unknown function	NA
114	PF3D7_0708500	Pf3D7_07_v3	385583	-	2739	-0.737	-1.370	-0.105	6.652	-3.415	1.58e-03	5.35e-02	-1.331	heat shock protein 86 family protein	NA
69	PF3D7_0513600	Pf3D7_05_v3	574941	-	3565	-1.045	-1.363	-0.726	5.614	-3.413	1.61e-03	5.39e-02	-1.279	deoxyribodipyrimidine photo-lyase, putative	NA
210	PF3D7_1115200	Pf3D7_11_v3	576773	+	3504	-0.659	-1.554	0.236	8.247	-3.404	1.63e-03	5.39e-02	-1.438	histone-lysine N-methyltransferase SET7	SET7
229	PF3D7_1145500	Pf3D7_11_v3	1807359	+	2772	1.102	0.252	1.951	1.564	3.404	1.63e-03	5.39e-02	-1.164	ABC transporter B family member 3, putative	ABCB3
59	PF3D7_0501300	Pf3D7_05_v3	68930	+	1184	-0.925	-1.601	-0.250	12.486	-3.399	1.71e-03	5.59e-02	-1.510	skeleton-binding protein 1	SBP1
246	PF3D7_1225600	Pf3D7_12_v3	1035261	-	2895	-0.478	-2.453	1.498	8.007	-3.386	1.71e-03	5.59e-02	-1.479	conserved Plasmodium protein, unknown function	NA
324	PF3D7_1417600	Pf3D7_14_v3	730694	-	13989	-0.568	-1.358	0.222	8.915	-3.382	1.73e-03	5.59e-02	-1.516	conserved Plasmodium protein, unknown function	NA
297	PF3D7_1345200	Pf3D7_13_v3	1812220	-	1710	1.084	0.716	1.452	3.402	3.379	1.74e-03	5.59e-02	-1.225	rhomboid protease ROM6, putative	ROM6
29	PF3D7_0310800	Pf3D7_03_v3	464662	+	330	0.487	-0.214	1.187	6.132	3.360	1.84e-03	5.68e-02	-1.434	conserved Plasmodium protein, unknown function	NA
122	PF3D7_0712900	Pf3D7_07_v3	590326	-	7408	-1.100	-1.332	-0.869	4.206	-3.367	1.80e-03	5.68e-02	-1.291	erythrocyte membrane protein 1, PfEMP1	VAR
190	PF3D7_1025000	Pf3D7_10_v3	1045608	-	4153	-0.570	-0.985	-0.156	8.252	-3.366	1.80e-03	5.68e-02	-1.528	formin 2, putative	NA
212	PF3D7_1119200	Pf3D7_11_v3	722717	-	573	-1.038	-1.443	-0.632	3.783	-3.361	1.83e-03	5.68e-02	-1.277	conserved protein, unknown function	NA
218	PF3D7_1124800	Pf3D7_11_v3	976880	-	1057	-0.568	-1.158	0.023	6.670	-3.363	1.82e-03	5.68e-02	-1.464	nuclear preribosomal assembly protein, putative	NA
234	PF3D7_1206300	Pf3D7_12_v3	281020	-	8283	-1.407	-1.752	-1.062	1.456	-3.354	1.87e-03	5.73e-02	-1.281	conserved Plasmodium protein, unknown function	NA
50	PF3D7_0416100	Pf3D7_04_v3	706529	+	2481	-0.909	-1.422	-0.396	4.248	-3.345	1.91e-03	5.78e-02	-1.356	glutamyl-tRNA(Gln) amidotransferase subunit A	GATA
106	PF3D7_0700100	Pf3D7_07_v3	20307	+	7777	-1.044	-1.871	-0.217	5.158	-3.344	1.93e-03	5.78e-02	-1.407	erythrocyte membrane protein 1, PfEMP1	VAR
203	PF3D7_1103400	Pf3D7_11_v3	146427	+	4389	1.198	-0.028	2.425	3.263	3.343	1.93e-03	5.78e-02	-1.308	FeS cluster assembly protein SufD, putative	SufD
42	PF3D7_0405400	Pf3D7_04_v3	291251	+	9726	-0.562	-1.533	0.410	10.748	-3.333	1.97e-03	5.87e-02	-1.659	pre-mRNA-processing-splicing factor 8, putative	PRPF8
56	PF3D7_0421300	Pf3D7_04_v3	969031	-	7561	-1.056	-1.582	-0.531	4.877	-3.320	2.05e-03	5.87e-02	-1.443	erythrocyte membrane protein 1, PfEMP1	VAR
247	PF3D7_1226600	Pf3D7_12_v3	1077868	-	909	1.498	0.096	2.900	-0.283	3.319	2.05e-03	5.87e-02	-1.410	proliferating cell nuclear antigen 2	PCNA2
255	PF3D7_1234500	Pf3D7_12_v3	1439896	-	1155	0.626	0.114	1.138	4.918	3.325	2.02e-03	5.87e-02	-1.431	conserved Plasmodium protein, unknown function	NA
308	PF3D7_1364000	Pf3D7_13_v3	2564625	+	2484	0.987	0.420	1.554	3.797	3.328	2.01e-03	5.87e-02	-1.366	conserved Plasmodium protein, unknown function	NA
313	PF3D7_1372100	Pf3D7_13_v3	2837053	+	2006	3.129	2.299	3.958	1.578	3.365	2.06e-03	5.87e-02	-1.337	Plasmodium exported protein (PHISTb), unknown function	GEXP04
339	PF3D7_1445800	Pf3D7_14_v3	1878658	-	3920	1.067	0.776	1.358	1.539	3.321	2.05e-03	5.87e-02	-1.356	conserved Plasmodium membrane protein, unknown function	NA
280	PF3D7_1307700	Pf3D7_13_v3	344525	+	3708	0.582	-0.368	1.531	6.383	3.313	2.09e-03	5.94e-02	-1.576	conserved Plasmodium protein, unknown function	NA
109	PF3D7_0703400	Pf3D7_07_v3	129370	-	2463	1.161	0.838	1.484	3.395	3.307	2.12e-03	5.99e-02	-1.403	conserved Plasmodium protein, unknown function	NA
183	PF3D7_1016100	Pf3D7_10_v3	643558	-	774	1.160	0.663	1.658	0.683	3.303	2.15e-03	6.01e-02	-1.411	conserved Plasmodium protein, unknown function	NA
358	PF3D7_1477700	Pf3D7_14_v3	3202931	+	1087	2.091	1.317	2.865	1.770	3.316	2.17e-03	6.04e-02	-1.395	Plasmodium exported protein (PHISTa), unknown function	Pfg14-748
64	PF3D7_0508700	Pf3D7_05_v3	358261	+	4473	-0.499	-1.326	0.327	7.639	-3.287	2.24e-03	6.05e-02	-1.715	pre-mRNA-processing ATP-dependent RNA helicase PRP5, putative	PRP5
144	PF3D7_0814100	Pf3D7_08_v3	682518	-	1055	0.938	-0.783	2.659	4.348	3.287	2.24e-03	6.05e-02	-1.489	conserved Plasmodium protein, unknown function	NA
178	PF3D7_1009300	Pf3D7_10_v3	377906	-	1803	1.211	0.885	1.536	3.019	3.287	2.24e-03	6.05e-02	-1.439	conserved Plasmodium protein, unknown function	NA
295	PF3D7_1344200	Pf3D7_13_v3	1769129	+	2799	-0.564	-1.236	0.108	9.434	-3.286	2.25e-03	6.05e-02	-1.770	heat shock protein 110, putative	HSP110
330	PF3D7_1427200	Pf3D7_14_v3	1061805	+	975	-1.619	-2.155	-1.082	1.505	-3.289	2.25e-03	6.05e-02	-1.430	selenoprotein	Sel4
44	PF3D7_0412400	Pf3D7_04_v3	545987	-	7824	-0.919	-1.577	-0.261	3.465	-3.283	2.27e-03	6.06e-02	-1.456	erythrocyte membrane protein 1, PfEMP1	VAR
32	PF3D7_0317100	Pf3D7_03_v3	686282	+	3201	0.874	0.596	1.152	2.504	3.274	2.33e-03	6.06e-02	-1.463	6-cysteine protein	B9
82	PF3D7_0531000	Pf3D7_05_v3	1267410	+	2130	0.713	-0.601	2.027	4.964	3.276	2.31e-03	6.06e-02	-1.555	conserved Plasmodium protein, unknown function	NA
134	PF3D7_0800300	Pf3D7_08_v3	40948	+	9992	-1.073	-1.392	-0.753	5.027	-3.282	2.29e-03	6.06e-02	-1.549	erythrocyte membrane protein 1, PfEMP1	VAR
289	PF3D7_1321700	Pf3D7_13_v3	902383	+	2784	-0.538	-0.896	-0.181	9.122	-3.276	2.31e-03	6.06e-02	-1.792	splicing factor 1	SF1
273	PF3D7_1302700	Pf3D7_13_v3	145174	+	5025	-0.474	-1.190	0.241	8.882	-3.270	2.35e-03	6.09e-02	-1.802	ATP-dependent RNA helicase DHR1, putative	NA
169	PF3D7_0926500	Pf3D7_09_v3	1075915	-	5769	1.173	0.733	1.614	0.469	3.256	2.44e-03	6.26e-02	-1.520	conserved Plasmodium protein, unknown function	NA
221	PF3D7_1128100	Pf3D7_11_v3	1094909	-	1023	-0.703	-1.004	-0.402	5.252	-3.253	2.46e-03	6.26e-02	-1.631	prefoldin subunit 5, putative	NA
233	PF3D7_1205700	Pf3D7_12_v3	253155	+	969	1.229	0.775	1.684	0.855	3.254	2.45e-03	6.26e-02	-1.517	targeted glyoxalase II	tGloII
17	PF3D7_0209700	Pf3D7_02_v3	400153	-	1707	0.555	-0.119	1.228	8.789	3.232	2.61e-03	6.32e-02	-1.893	RING zinc finger protein, putative	NA
22	PF3D7_0220500	Pf3D7_02_v3	823825	-	1040	-0.875	-2.077	0.327	6.458	-3.238	2.57e-03	6.32e-02	-1.752	Plasmodium exported protein (hyp2), unknown function	NA
87	PF3D7_0606800	Pf3D7_06_v3	288377	-	900	1.551	1.311	1.791	3.382	3.241	2.60e-03	6.32e-02	-1.571	probable protein, unknown function	NA
130	PF3D7_0723900	Pf3D7_07_v3	1000701	-	4046	-0.612	-0.899	-0.325	7.826	-3.238	2.57e-03	6.32e-02	-1.844	RNA-binding protein, putative	NA
187	PF3D7_1021900	Pf3D7_10_v3	905473	-	6873	-0.993	-1.349	-0.638	6.736	-3.246	2.57e-03	6.32e-02	-1.778	PHAX domain-containing protein, putative	NA
199	PF3D7_1100300	Pf3D7_11_v3	45056	+	1178	1.993	1.575	2.412	-0.537	3.236	2.60e-03	6.32e-02	-1.602	rifin	RIF
241	PF3D7_1217000	Pf3D7_12_v3	674349	-	429	1.119	0.313	1.924	1.672	3.236	2.58e-03	6.32e-02	-1.547	conserved Plasmodium protein, unknown function	NA
317	PF3D7_1401600	Pf3D7_14_v3	61364	-	1625	-0.760	-1.042	-0.478	8.852	-3.236	2.61e-03	6.32e-02	-1.894	Plasmodium exported protein (PHISTb), unknown function	NA
70	PF3D7_0518300	Pf3D7_05_v3	759831	-	1168	-0.484	-0.912	-0.056	6.571	-3.226	2.65e-03	6.33e-02	-1.804	proteasome subunit beta type-1, putative	NA
72	PF3D7_0521000	Pf3D7_05_v3	859373	-	1691	-0.687	-1.390	0.017	5.971	-3.225	2.66e-03	6.33e-02	-1.757	conserved Plasmodium protein, unknown function	NA
98	PF3D7_0621500	Pf3D7_06_v3	881963	+	1032	1.065	0.072	2.058	1.161	3.225	2.65e-03	6.33e-02	-1.575	ribonuclease P/MRP protein subunit RPP1, putative	RPP1
174	PF3D7_0936800	Pf3D7_09_v3	1458392	+	1471	-0.876	-1.190	-0.562	10.878	-3.220	2.77e-03	6.48e-02	-1.951	Plasmodium exported protein (PHISTc), unknown function	NA
181	PF3D7_1013000	Pf3D7_10_v3	500210	+	2012	1.140	0.529	1.751	2.844	3.208	2.78e-03	6.48e-02	-1.622	zinc finger protein, putative	NA
184	PF3D7_1016200	Pf3D7_10_v3	646054	+	1683	1.055	0.321	1.789	4.570	3.206	2.80e-03	6.48e-02	-1.706	Rab3 GTPase-activating protein non-catalytic subunit, putative	NA
227	PF3D7_1140800	Pf3D7_11_v3	1633920	+	2412	0.505	-0.045	1.055	6.676	3.212	2.75e-03	6.48e-02	-1.843	conserved Plasmodium protein, unknown function	NA
230	PF3D7_1149500	Pf3D7_11_v3	1991359	-	2660	-0.653	-1.498	0.192	8.007	-3.204	2.81e-03	6.48e-02	-1.921	ring-infected erythrocyte surface antigen 2, pseudogene	RESA2
319	PF3D7_1410500	Pf3D7_14_v3	423751	-	500	1.042	0.705	1.378	1.400	3.205	2.80e-03	6.48e-02	-1.619	conserved Plasmodium protein, unknown function	NA
104	PF3D7_0631600	Pf3D7_06_v3	1323294	+	1142	-1.234	-1.641	-0.828	2.559	-3.201	2.83e-03	6.49e-02	-1.630	exported protein family 4	EPF4
323	PF3D7_1414500	Pf3D7_14_v3	578369	-	9161	-0.636	-0.920	-0.351	7.984	-3.197	2.86e-03	6.52e-02	-1.959	atypical protein kinase, ABC-1 family, putative	ABCk2
12	PF3D7_0201800	Pf3D7_02_v3	86832	-	1960	-0.527	-0.803	-0.252	9.437	-3.178	3.02e-03	6.61e-02	-2.040	knob associated heat shock protein 40	KAHsp40
33	PF3D7_0317500	Pf3D7_03_v3	716523	-	5309	0.587	-0.080	1.253	7.115	3.180	3.00e-03	6.61e-02	-1.955	kinesin-5	EG5
52	PF3D7_0418300	Pf3D7_04_v3	819362	-	2979	0.610	0.114	1.106	10.470	3.186	2.95e-03	6.61e-02	-2.029	conserved Plasmodium protein, unknown function	NA
67	PF3D7_0511000	Pf3D7_05_v3	467585	-	516	-0.538	-0.738	-0.337	8.120	-3.185	2.96e-03	6.61e-02	-1.981	translationally-controlled tumor protein homolog	TCTP
263	PF3D7_1244300	Pf3D7_12_v3	1857849	+	242	-1.945	-2.961	-0.930	2.568	-3.199	2.97e-03	6.61e-02	-1.661	ACEA small nucleolar RNA U3	NA
277	PF3D7_1304300	Pf3D7_13_v3	231083	+	642	1.477	0.660	2.294	0.552	3.180	3.00e-03	6.61e-02	-1.685	conserved Plasmodium protein, unknown function	NA
278	PF3D7_1305400	Pf3D7_13_v3	268785	-	1953	0.561	0.218	0.904	5.309	3.182	2.98e-03	6.61e-02	-1.816	AAR2 protein, putative	NA
34	PF3D7_0319600	Pf3D7_03_v3	817913	+	783	-0.442	-0.957	0.073	8.336	-3.170	3.08e-03	6.72e-02	-2.039	elongation factor 1 (EF-1), putative	NA
195	PF3D7_1035800	Pf3D7_10_v3	1420533	+	2139	-1.293	-1.677	-0.909	9.469	-3.201	3.10e-03	6.72e-02	-2.001	probable protein, unknown function	M712
283	PF3D7_1309400	Pf3D7_13_v3	431892	+	3984	-0.750	-1.414	-0.086	5.757	-3.166	3.12e-03	6.72e-02	-1.880	HORMA domain protein, putative	NA
173	PF3D7_0935900	Pf3D7_09_v3	1420483	-	2325	-0.762	-1.083	-0.440	13.744	-3.169	3.13e-03	6.73e-02	-2.065	ring-exported protein 1	REX1
152	PF3D7_0829100	Pf3D7_08_v3	1252349	+	1448	-0.521	-1.286	0.244	7.060	-3.160	3.16e-03	6.75e-02	-2.000	conserved protein, unknown function	NA
222	PF3D7_1133000	Pf3D7_11_v3	1275574	+	90	1.310	0.942	1.678	0.955	3.158	3.18e-03	6.77e-02	-1.728	conserved Plasmodium protein, unknown function	NA
16	PF3D7_0205400	Pf3D7_02_v3	223478	+	1374	0.446	0.105	0.787	6.179	3.149	3.26e-03	6.80e-02	-1.963	PCI domain-containing protein, putative	NA
55	PF3D7_0420000	Pf3D7_04_v3	894612	-	10113	-0.524	-1.375	0.327	9.311	-3.146	3.29e-03	6.80e-02	-2.119	zinc finger protein, putative	NA
182	PF3D7_1015800	Pf3D7_10_v3	633682	+	1605	1.197	0.525	1.870	0.318	3.151	3.24e-03	6.80e-02	-1.750	ribonucleoside-diphosphate reductase small chain, putative	NA
258	PF3D7_1240400	Pf3D7_12_v3	1704512	+	7979	-0.936	-1.157	-0.715	4.827	-3.148	3.27e-03	6.80e-02	-1.853	erythrocyte membrane protein 1, PfEMP1	VAR
355	PF3D7_1468100	Pf3D7_14_v3	2786308	-	8016	-0.558	-0.954	-0.161	10.206	-3.146	3.28e-03	6.80e-02	-2.127	conserved Plasmodium protein, unknown function	NA
357	PF3D7_1472300	Pf3D7_14_v3	2954108	+	3001	1.050	0.167	1.932	4.451	3.145	3.30e-03	6.80e-02	-1.839	conserved Plasmodium membrane protein, unknown function	NA
66	PF3D7_0509800	Pf3D7_05_v3	410268	+	5041	-0.385	-0.757	-0.013	8.254	-3.141	3.33e-03	6.80e-02	-2.107	phosphatidylinositol 4-kinase	PI4K
232	PF3D7_1200200	Pf3D7_12_v3	26321	-	1367	-1.845	-2.273	-1.417	-0.252	-3.141	3.33e-03	6.80e-02	-1.800	rifin	RIF
226	PF3D7_1140200	Pf3D7_11_v3	1601257	-	1822	-1.160	-1.579	-0.742	3.820	-3.140	3.35e-03	6.81e-02	-1.823	conserved Plasmodium protein, unknown function	NA
348	PF3D7_1457100	Pf3D7_14_v3	2340784	+	2244	-0.895	-1.549	-0.240	6.629	-3.139	3.39e-03	6.85e-02	-2.007	conserved Plasmodium protein, unknown function	NA
200	PF3D7_1102600	Pf3D7_11_v3	123818	-	919	1.461	0.883	2.039	2.317	3.132	3.43e-03	6.91e-02	-1.790	Plasmodium exported protein, unknown function	GEXP14
112	PF3D7_0705600	Pf3D7_07_v3	281035	-	3399	0.833	0.363	1.303	3.988	3.125	3.48e-03	6.96e-02	-1.853	RNA helicase, putative	NA
352	PF3D7_1460500	Pf3D7_14_v3	2466091	+	4899	1.016	0.429	1.604	2.431	3.123	3.49e-03	6.96e-02	-1.806	conserved Plasmodium protein, unknown function	NA
3	PF3D7_0101000	Pf3D7_01_v3	65817	-	1173	-2.246	-2.928	-1.565	-1.073	-3.119	3.57e-03	7.06e-02	-1.886	rifin	RIF
90	PF3D7_0609700	Pf3D7_06_v3	413652	+	6130	-0.563	-1.557	0.430	9.552	-3.111	3.61e-03	7.06e-02	-2.204	conserved Plasmodium protein, unknown function	NA
186	PF3D7_1019300	Pf3D7_10_v3	774929	-	5559	0.842	0.580	1.103	4.369	3.114	3.58e-03	7.06e-02	-1.899	zinc finger protein, putative	NA
272	PF3D7_1301400	Pf3D7_13_v3	82718	+	1301	-0.891	-1.162	-0.619	8.053	-3.118	3.61e-03	7.06e-02	-2.123	Plasmodium exported protein (hyp12), unknown function	HYP12
165	PF3D7_0915500	Pf3D7_09_v3	657418	+	1995	1.320	0.789	1.851	0.044	3.109	3.63e-03	7.07e-02	-1.849	conserved Plasmodium protein, unknown function	NA
123	PF3D7_0713500	Pf3D7_07_v3	614385	+	2865	0.925	0.534	1.316	4.314	3.100	3.72e-03	7.07e-02	-1.935	conserved Plasmodium protein, unknown function	NA
141	PF3D7_0808700	Pf3D7_08_v3	440408	+	7655	-0.981	-1.345	-0.618	4.547	-3.102	3.69e-03	7.07e-02	-1.948	erythrocyte membrane protein 1, PfEMP1	VAR
145	PF3D7_0817100	Pf3D7_08_v3	774299	+	2493	1.043	0.215	1.870	0.070	3.101	3.70e-03	7.07e-02	-1.866	tRNA modification GTPase, putative	NA
162	PF3D7_0913100	Pf3D7_09_v3	571031	-	2319	1.169	0.432	1.905	-0.164	3.102	3.69e-03	7.07e-02	-1.868	conserved Plasmodium protein, unknown function	NA
345	PF3D7_1451100	Pf3D7_14_v3	2090902	+	2499	-0.648	-1.295	-0.001	12.559	-3.105	3.67e-03	7.07e-02	-2.224	elongation factor 2	eEF2
281	PF3D7_1308300	Pf3D7_13_v3	372260	+	387	0.444	-0.083	0.971	7.958	3.092	3.80e-03	7.19e-02	-2.215	40S ribosomal protein S27	RPS27
27	PF3D7_0304900	Pf3D7_03_v3	231793	-	513	0.801	0.116	1.486	5.085	3.080	3.92e-03	7.22e-02	-2.030	conserved Plasmodium protein, unknown function	NA
76	PF3D7_0524800	Pf3D7_05_v3	1021408	-	2900	0.882	0.028	1.736	3.247	3.087	3.84e-03	7.22e-02	-1.912	ubiquitin fusion degradation protein 1, putative	UFD1
225	PF3D7_1137300	Pf3D7_11_v3	1466197	-	2070	0.450	-0.267	1.166	7.350	3.080	3.92e-03	7.22e-02	-2.212	CLPTM1 domain-containing protein, putative	NA
252	PF3D7_1231600	Pf3D7_12_v3	1301098	-	3507	-0.706	-1.747	0.336	6.288	-3.084	3.88e-03	7.22e-02	-2.134	pre-mRNA-splicing factor ATP-dependent RNA helicase PRP2, putative	PRP2
282	PF3D7_1309100	Pf3D7_13_v3	418820	+	1302	-0.722	-1.280	-0.165	8.832	-3.088	3.87e-03	7.22e-02	-2.260	60S ribosomal protein L24, putative	NA
291	PF3D7_1324200	Pf3D7_13_v3	1000100	-	1783	-0.797	-1.141	-0.454	7.145	-3.086	3.89e-03	7.22e-02	-2.185	micro-fibrillar-associated protein, putative	NA
119	PF3D7_0712300	Pf3D7_07_v3	542906	-	7615	-1.223	-2.264	-0.181	3.752	-3.079	3.97e-03	7.25e-02	-1.967	erythrocyte membrane protein 1, PfEMP1	VAR
307	PF3D7_1362300	Pf3D7_13_v3	2493143	+	570	0.782	-0.312	1.876	3.668	3.075	3.97e-03	7.25e-02	-1.957	conserved protein, unknown function	NA
240	PF3D7_1215900	Pf3D7_12_v3	641552	+	1968	0.743	0.298	1.187	4.806	3.068	4.04e-03	7.35e-02	-2.049	serpentine receptor, putative	SR10
20	PF3D7_0216400	Pf3D7_02_v3	675431	+	2169	0.789	0.122	1.457	0.530	3.064	4.09e-03	7.37e-02	-1.936	vacuolar protein sorting-associated protein 45, putative	VPS45
172	PF3D7_0932900	Pf3D7_09_v3	1309467	-	477	0.939	0.530	1.349	2.103	3.065	4.08e-03	7.37e-02	-1.933	conserved Plasmodium protein, unknown function	NA
292	PF3D7_1326700	Pf3D7_13_v3	1125280	+	1629	1.336	0.904	1.768	3.634	3.063	4.16e-03	7.46e-02	-1.994	conserved Apicomplexan protein, unknown function	NA
160	PF3D7_0907900	Pf3D7_09_v3	367865	-	925	-1.480	-2.225	-0.735	3.656	-3.067	4.19e-03	7.48e-02	-2.003	peptide deformylase	PDF
333	PF3D7_1434300	Pf3D7_14_v3	1372903	+	1695	-0.408	-1.424	0.608	8.746	-3.050	4.25e-03	7.55e-02	-2.345	Hsp70/Hsp90 organizing protein	HOP
353	PF3D7_1462800	Pf3D7_14_v3	2559098	+	1250	-0.693	-1.932	0.546	13.081	-3.050	4.27e-03	7.56e-02	-2.357	glyceraldehyde-3-phosphate dehydrogenase	GAPDH
5	PF3D7_0108500	Pf3D7_01_v3	349170	+	540	-0.875	-2.335	0.586	10.163	-3.051	4.39e-03	7.58e-02	-2.374	conserved Plasmodium protein, unknown function	NA
10	PF3D7_0200100	Pf3D7_02_v3	25232	+	5937	-1.299	-2.059	-0.540	3.963	-3.049	4.33e-03	7.58e-02	-2.040	erythrocyte membrane protein 1, PfEMP1	VAR
214	PF3D7_1122300	Pf3D7_11_v3	846929	+	1086	0.944	0.421	1.466	3.809	3.043	4.32e-03	7.58e-02	-2.043	conserved Plasmodium protein, unknown function	NA
215	PF3D7_1122900	Pf3D7_11_v3	878969	+	16305	-1.086	-1.508	-0.664	1.411	-3.039	4.37e-03	7.58e-02	-1.987	dynein heavy chain, putative	NA
254	PF3D7_1233100	Pf3D7_12_v3	1359169	+	408	-0.794	-1.469	-0.119	4.068	-3.041	4.35e-03	7.58e-02	-2.047	conserved protein, unknown function	NA
270	PF3D7_1253100	Pf3D7_12_v3	2171342	+	1008	0.614	0.151	1.077	6.992	3.039	4.37e-03	7.58e-02	-2.289	Plasmodium exported protein (PHISTa), unknown function	NA
115	PF3D7_0709600	Pf3D7_07_v3	429857	-	3902	-0.489	-0.848	-0.129	7.337	-3.035	4.41e-03	7.59e-02	-2.319	ribonucleases P/MRP protein subunit POP1, putative	POP1
223	PF3D7_1133700	Pf3D7_11_v3	1302173	+	3815	-0.680	-1.110	-0.249	10.033	-3.034	4.46e-03	7.60e-02	-2.405	FHA domain-containing protein, putative	NA
264	PF3D7_1244800	Pf3D7_12_v3	1873194	-	2094	-0.452	-2.303	1.399	7.567	-3.030	4.48e-03	7.60e-02	-2.349	cytoplasmic translation machinery associated protein, putative	NA
269	PF3D7_1251400	Pf3D7_12_v3	2097436	-	1410	1.035	0.691	1.379	1.657	3.031	4.46e-03	7.60e-02	-2.003	conserved Plasmodium protein, unknown function	NA
48	PF3D7_0415300	Pf3D7_04_v3	681810	+	4159	-0.547	-0.925	-0.169	8.627	-3.020	4.59e-03	7.68e-02	-2.412	cdc2-related protein kinase 3	CRK3
108	PF3D7_0703200	Pf3D7_07_v3	122513	-	4623	-0.955	-1.527	-0.383	4.508	-3.017	4.63e-03	7.68e-02	-2.149	conserved Plasmodium protein, unknown function	NA
118	PF3D7_0712000	Pf3D7_07_v3	527338	-	7794	-1.572	-1.966	-1.178	3.236	-3.029	4.61e-03	7.68e-02	-2.056	erythrocyte membrane protein 1, PfEMP1	VAR
155	PF3D7_0833500	Pf3D7_08_v3	1435794	-	7656	-0.978	-1.408	-0.547	4.340	-3.022	4.57e-03	7.68e-02	-2.118	erythrocyte membrane protein 1, PfEMP1	VAR
188	PF3D7_1023000	Pf3D7_10_v3	961066	-	1242	0.838	0.065	1.610	1.337	3.016	4.65e-03	7.68e-02	-2.034	conserved Plasmodium membrane protein, unknown function	NA
300	PF3D7_1347500	Pf3D7_13_v3	1897983	-	1380	-0.472	-0.748	-0.196	12.054	-3.015	4.65e-03	7.68e-02	-2.447	DNA/RNA-binding protein Alba 4	ALBA4
318	PF3D7_1404900	Pf3D7_14_v3	170000	+	894	0.405	-0.046	0.855	8.338	3.020	4.59e-03	7.68e-02	-2.403	conserved Plasmodium protein, unknown function	NA
92	PF3D7_0613600	Pf3D7_06_v3	554457	+	3772	1.236	0.284	2.188	0.053	3.009	4.73e-03	7.71e-02	-2.057	conserved Plasmodium protein, unknown function	NA
125	PF3D7_0716000	Pf3D7_07_v3	703207	+	3378	-0.490	-0.849	-0.130	8.568	-3.008	4.74e-03	7.71e-02	-2.441	RNA-binding protein, putative	NA
167	PF3D7_0923100	Pf3D7_09_v3	941830	-	669	1.113	0.506	1.720	1.302	3.009	4.73e-03	7.71e-02	-2.049	OTU domain-containing protein, putative	NA
239	PF3D7_1214600	Pf3D7_12_v3	613561	-	1014	-0.563	-1.043	-0.084	4.766	-3.012	4.70e-03	7.71e-02	-2.173	adrenodoxin-type ferredoxin, putative	NA
100	PF3D7_0625400	Pf3D7_06_v3	1032536	-	1239	0.554	-0.780	1.888	7.778	3.005	4.77e-03	7.73e-02	-2.409	conserved Plasmodium protein, unknown function	NA
79	PF3D7_0528100	Pf3D7_05_v3	1157840	-	3714	-0.377	-1.096	0.342	9.370	-2.997	4.88e-03	7.81e-02	-2.484	AP-1 complex subunit beta, putative	NA
191	PF3D7_1025500	Pf3D7_10_v3	1067652	-	19341	-1.108	-1.901	-0.316	0.450	-2.998	4.86e-03	7.81e-02	-2.075	conserved Plasmodium protein, unknown function	NA
194	PF3D7_1030100	Pf3D7_10_v3	1224519	-	4574	-0.406	-1.677	0.865	8.759	-2.997	4.88e-03	7.81e-02	-2.471	pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22, putative	PRP22
77	PF3D7_0527500	Pf3D7_05_v3	1143618	+	1742	-0.398	-1.848	1.052	9.586	-2.992	4.94e-03	7.83e-02	-2.498	Hsc70-interacting protein	HIP
131	PF3D7_0724000	Pf3D7_07_v3	1006335	+	5811	0.875	0.418	1.332	2.241	2.994	4.92e-03	7.83e-02	-2.092	Rab GTPase activator and protein kinase, putative	NA
268	PF3D7_1250800	Pf3D7_12_v3	2077718	+	5170	-0.475	-0.773	-0.177	6.852	-2.991	4.95e-03	7.83e-02	-2.396	DNA repair protein rhp16, putative	NA
340	PF3D7_1446300	Pf3D7_14_v3	1898351	+	3576	1.129	0.535	1.724	4.066	2.990	5.01e-03	7.90e-02	-2.187	conserved Plasmodium membrane protein, unknown function	NA
179	PF3D7_1011800	Pf3D7_10_v3	455398	+	3420	-0.579	-1.305	0.146	10.624	-2.984	5.04e-03	7.92e-02	-2.524	PRE-binding protein	PREBP
274	PF3D7_1302900	Pf3D7_13_v3	154992	+	2403	1.025	0.147	1.903	3.537	2.980	5.10e-03	7.98e-02	-2.173	conserved Plasmodium protein, unknown function	NA
235	PF3D7_1208600	Pf3D7_12_v3	402300	+	228	-0.700	-1.229	-0.171	3.757	-2.977	5.15e-03	8.00e-02	-2.202	mitochondrial import inner membrane translocase subunit TIM10, putative	TIM10
284	PF3D7_1309600	Pf3D7_13_v3	438510	+	867	0.727	0.325	1.129	4.309	2.976	5.15e-03	8.00e-02	-2.223	ribosomal RNA methyltransferase, putative	NA
11	PF3D7_0201600	Pf3D7_02_v3	77251	-	1558	-0.649	-1.469	0.172	9.150	-2.971	5.23e-03	8.01e-02	-2.527	PHISTb domain-containing RESA-like protein 1	RLP1
18	PF3D7_0211800	Pf3D7_02_v3	475242	+	1833	-0.643	-1.218	-0.068	9.283	-2.961	5.37e-03	8.01e-02	-2.569	asparagine–tRNA ligase	AsnRS
97	PF3D7_0621300	Pf3D7_06_v3	873809	+	2382	0.443	-0.422	1.307	7.592	2.960	5.37e-03	8.01e-02	-2.512	mRNA binding Pumilio-homology domain protein, putative	NA
129	PF3D7_0719900	Pf3D7_07_v3	865927	+	10206	-0.417	-1.081	0.248	7.724	-2.959	5.39e-03	8.01e-02	-2.527	conserved Plasmodium membrane protein, unknown function	NA
135	PF3D7_0801700	Pf3D7_08_v3	112299	+	5579	-0.589	-0.932	-0.246	6.129	-2.966	5.29e-03	8.01e-02	-2.402	sentrin-specific protease 2, putative	SENP2
137	PF3D7_0804700	Pf3D7_08_v3	271417	-	5997	-0.573	-1.463	0.317	5.755	-2.962	5.34e-03	8.01e-02	-2.376	conserved Plasmodium protein, unknown function	NA
159	PF3D7_0907700	Pf3D7_09_v3	364069	-	840	0.415	0.186	0.645	7.929	2.970	5.23e-03	8.01e-02	-2.506	subunit of proteaseome activator complex, putative	PA28
217	PF3D7_1124100	Pf3D7_11_v3	951382	-	4962	-0.411	-0.946	0.123	8.014	-2.963	5.34e-03	8.01e-02	-2.532	beige/BEACH domain protein, putative	NA
256	PF3D7_1235300	Pf3D7_12_v3	1470713	+	4989	-0.568	-1.359	0.222	9.292	-2.966	5.29e-03	8.01e-02	-2.553	CCR4-NOT transcription complex subunit 4, putative	NOT4
301	PF3D7_1350100	Pf3D7_13_v3	2005962	-	1989	-0.430	-1.427	0.567	9.206	-2.962	5.34e-03	8.01e-02	-2.565	lysine–tRNA ligase	KRS1
312	PF3D7_1366500	Pf3D7_13_v3	2661573	+	450	1.090	0.675	1.506	0.730	2.968	5.26e-03	8.01e-02	-2.136	nucleoside diphosphate kinase	NDK
350	PF3D7_1458000	Pf3D7_14_v3	2387786	+	1710	0.339	-0.118	0.796	8.196	2.974	5.19e-03	8.01e-02	-2.506	cysteine proteinase falcipain 1	FP1
61	PF3D7_0502500	Pf3D7_05_v3	114149	+	1785	1.611	0.861	2.360	0.201	2.957	5.42e-03	8.02e-02	-2.162	conserved Plasmodium protein, unknown function	NA
354	PF3D7_1466300	Pf3D7_14_v3	2709418	+	3775	-0.392	-1.138	0.353	9.366	-2.954	5.46e-03	8.05e-02	-2.587	26S proteasome regulatory subunit RPN2, putative	RPN2
151	PF3D7_0826900	Pf3D7_08_v3	1164655	+	2551	0.987	0.185	1.788	3.078	2.949	5.54e-03	8.14e-02	-2.213	conserved Plasmodium protein, unknown function	NA
80	PF3D7_0528800	Pf3D7_05_v3	1180425	-	1614	0.476	-0.329	1.281	6.073	2.942	5.64e-03	8.23e-02	-2.448	nucleolar preribosomal GTPase, putative	NA
257	PF3D7_1239800	Pf3D7_12_v3	1660451	+	17304	-1.106	-1.531	-0.682	3.686	-2.944	5.62e-03	8.23e-02	-2.271	conserved Plasmodium protein, unknown function	NA
39	PF3D7_0404300	Pf3D7_04_v3	234014	-	3000	-0.853	-1.708	0.001	7.533	-2.947	5.68e-03	8.23e-02	-2.553	conserved Plasmodium protein, unknown function	NA
185	PF3D7_1019100	Pf3D7_10_v3	766168	-	5787	-1.392	-1.726	-1.058	0.749	-2.939	5.67e-03	8.23e-02	-2.197	conserved Plasmodium protein, unknown function	NA
304	PF3D7_1355200	Pf3D7_13_v3	2191058	-	3054	1.630	0.890	2.370	0.536	2.939	5.71e-03	8.24e-02	-2.201	RAP protein, putative	NA
328	PF3D7_1424500	Pf3D7_14_v3	979464	+	142	-0.825	-1.714	0.063	3.590	-2.929	5.82e-03	8.37e-02	-2.269	small nucleolar RNA snoR27	NA
293	PF3D7_1338600	Pf3D7_13_v3	1556659	-	3076	1.267	0.697	1.837	0.039	2.928	5.85e-03	8.39e-02	-2.224	conserved Plasmodium protein, unknown function	NA
311	PF3D7_1366000	Pf3D7_13_v3	2635213	+	276	1.117	0.785	1.450	2.202	2.924	5.91e-03	8.45e-02	-2.245	conserved Plasmodium protein, unknown function	NA
236	PF3D7_1210300	Pf3D7_12_v3	465115	+	630	0.713	-0.071	1.498	3.554	2.919	5.97e-03	8.51e-02	-2.306	conserved Plasmodium protein, unknown function	NA
249	PF3D7_1228900	Pf3D7_12_v3	1180670	-	4814	-0.607	-1.072	-0.142	6.434	-2.916	6.03e-03	8.56e-02	-2.543	conserved Plasmodium protein, unknown function	NA
8	PF3D7_0115200	Pf3D7_01_v3	591849	+	1339	-2.053	-3.146	-0.961	-0.691	-2.917	6.08e-03	8.59e-02	-2.273	rifin	RIF
30	PF3D7_0311700	Pf3D7_03_v3	502698	+	3151	-1.459	-2.316	-0.601	0.983	-2.910	6.12e-03	8.59e-02	-2.258	plasmepsin VI	NA
46	PF3D7_0412900	Pf3D7_04_v3	576810	-	7859	-1.189	-1.516	-0.862	2.611	-2.911	6.10e-03	8.59e-02	-2.281	erythrocyte membrane protein 1, PfEMP1	VAR
43	PF3D7_0411900	Pf3D7_04_v3	528192	-	6294	-0.914	-1.287	-0.541	1.934	-2.905	6.20e-03	8.62e-02	-2.285	DNA polymerase alpha catalytic subunit A	NA
201	PF3D7_1102700	Pf3D7_11_v3	128789	+	276	-0.587	-0.982	-0.192	10.475	-2.905	6.20e-03	8.62e-02	-2.712	early transcribed membrane protein 11.1	ETRAMP11.1
279	PF3D7_1306400	Pf3D7_13_v3	297178	-	1182	-0.466	-1.327	0.396	7.247	-2.904	6.22e-03	8.62e-02	-2.620	26S protease regulatory subunit 10B, putative	RPT4
302	PF3D7_1353500	Pf3D7_13_v3	2144125	+	981	0.778	0.133	1.423	3.030	2.907	6.17e-03	8.62e-02	-2.310	RNA polymerase II transcription factor B subunit 4, putative	TFB4
2	mal_rna_17:rRNA	M76611	5577	-	195	-1.264	-1.671	-0.857	4.223	-2.903	6.33e-03	8.72e-02	-2.368	NA	NA
196	PF3D7_1037900	Pf3D7_10_v3	1502955	-	1368	1.025	0.342	1.708	2.136	2.897	6.34e-03	8.72e-02	-2.305	conserved Plasmodium protein, unknown function	NA
164	PF3D7_0915100	Pf3D7_09_v3	643232	-	812	-0.531	-1.152	0.090	6.543	-2.889	6.46e-03	8.87e-02	-2.613	SUMO-conjugating enzyme UBC9	UBC9
35	PF3D7_0323000	Pf3D7_03_v3	968675	-	528	-0.901	-1.197	-0.604	4.269	-2.885	6.53e-03	8.91e-02	-2.451	translation machinery-associated protein 7, putative	TMA7
309	PF3D7_1365000	Pf3D7_13_v3	2608698	+	1047	-0.839	-1.102	-0.577	3.815	-2.886	6.52e-03	8.91e-02	-2.383	conserved Plasmodium protein, unknown function	NA
60	PF3D7_0501400	Pf3D7_05_v3	74509	+	5334	-1.045	-1.303	-0.787	10.998	-2.901	6.65e-03	8.95e-02	-2.750	interspersed repeat antigen	FIRA
75	PF3D7_0523700	Pf3D7_05_v3	980754	-	4601	1.308	0.350	2.266	0.920	2.876	6.69e-03	8.95e-02	-2.330	conserved Plasmodium membrane protein, unknown function	NA
86	PF3D7_0601600	Pf3D7_06_v3	68833	-	861	1.227	-0.183	2.636	1.035	2.873	6.74e-03	8.95e-02	-2.336	tetratricopeptide repeat protein, putative	NA
93	PF3D7_0613900	Pf3D7_06_v3	579435	-	6462	1.190	-0.386	2.767	0.943	2.874	6.72e-03	8.95e-02	-2.333	myosin E, putative	myoE
96	PF3D7_0618200	Pf3D7_06_v3	764667	-	826	-0.533	-1.152	0.086	7.015	-2.871	6.78e-03	8.95e-02	-2.694	conserved Plasmodium protein, unknown function	NA
101	PF3D7_0625600	Pf3D7_06_v3	1039655	+	1896	0.840	-0.298	1.979	5.615	2.878	6.67e-03	8.95e-02	-2.558	poly(A) polymerase PAP, putative	NA
163	PF3D7_0913200	Pf3D7_09_v3	575679	+	831	-0.503	-1.221	0.215	8.866	-2.871	6.77e-03	8.95e-02	-2.774	elongation factor 1-beta	EF-1beta
228	PF3D7_1142400	Pf3D7_11_v3	1702089	-	1554	0.593	-0.547	1.732	5.970	2.878	6.64e-03	8.95e-02	-2.595	coproporphyrinogen-III oxidase	CPO
276	PF3D7_1303100	Pf3D7_13_v3	159024	+	892	-0.764	-1.043	-0.485	3.651	-2.879	6.62e-03	8.95e-02	-2.425	methyltransferase-like protein, putative	NA
334	PF3D7_1436500	Pf3D7_14_v3	1488706	+	1296	1.054	0.135	1.972	0.183	2.873	6.73e-03	8.95e-02	-2.336	GTP-binding protein, putative	NA
110	PF3D7_0703700	Pf3D7_07_v3	146645	-	750	0.495	-0.380	1.370	7.579	2.868	6.82e-03	8.98e-02	-2.726	conserved Plasmodium protein, unknown function	NA
171	PF3D7_0931400	Pf3D7_09_v3	1263347	+	1484	-0.845	-1.123	-0.567	3.547	-2.862	6.93e-03	9.00e-02	-2.427	conserved Plasmodium protein, unknown function	NA
206	PF3D7_1108600	Pf3D7_11_v3	369675	-	1032	-0.677	-1.052	-0.302	9.227	-2.866	6.92e-03	9.00e-02	-2.788	endoplasmic reticulum-resident calcium binding protein	ERC
306	PF3D7_1360100	Pf3D7_13_v3	2405249	-	969	-0.524	-0.778	-0.270	5.582	-2.864	6.88e-03	9.00e-02	-2.577	RNA-binding protein, putative	NA
329	PF3D7_1426000	Pf3D7_14_v3	1016133	-	486	0.490	0.116	0.864	8.627	2.863	6.90e-03	9.00e-02	-2.783	60S ribosomal protein L21	RPL21
15	PF3D7_0202500	Pf3D7_02_v3	127994	+	321	-0.663	-1.051	-0.275	12.139	-2.862	6.99e-03	9.04e-02	-2.815	early transcribed membrane protein 2	ETRAMP2
157	PF3D7_0903100	Pf3D7_09_v3	130140	-	798	0.695	0.070	1.319	4.700	2.858	7.00e-03	9.04e-02	-2.518	protein RER1, putative	RER1
21	PF3D7_0218700	Pf3D7_02_v3	763491	-	1701	-0.606	-1.170	-0.042	7.123	-2.852	7.11e-03	9.05e-02	-2.732	pre-mRNA-processing protein 45, putative	PRP45
150	PF3D7_0826100	Pf3D7_08_v3	1113369	-	25776	-0.526	-0.989	-0.064	10.275	-2.853	7.08e-03	9.05e-02	-2.833	E3 ubiquitin-protein ligase, putative	NA
192	PF3D7_1027300	Pf3D7_10_v3	1140589	-	2014	-0.763	-1.045	-0.481	8.469	-2.857	7.12e-03	9.05e-02	-2.792	peroxiredoxin	nPrx
250	PF3D7_1229600	Pf3D7_12_v3	1214043	-	3673	-1.015	-1.610	-0.421	1.452	-2.855	7.06e-03	9.05e-02	-2.377	conserved Plasmodium protein, unknown function	NA
266	PF3D7_1247400	Pf3D7_12_v3	1955124	-	915	-0.628	-1.393	0.137	6.237	-2.853	7.10e-03	9.05e-02	-2.670	peptidyl-prolyl cis-trans isomerase FKBP35	FKBP35
78	PF3D7_0528000	Pf3D7_05_v3	1156205	-	375	0.784	-1.169	2.738	3.675	2.849	7.17e-03	9.08e-02	-2.468	proteasome maturation factor UMP1, putative	UMP1
91	PF3D7_0612700	Pf3D7_06_v3	525987	-	1044	0.819	-0.189	1.826	1.993	2.847	7.20e-03	9.08e-02	-2.403	6-cysteine protein	P12
325	PF3D7_1417700	Pf3D7_14_v3	750330	+	1355	-0.593	-0.956	-0.231	4.828	-2.846	7.21e-03	9.08e-02	-2.560	conserved Plasmodium protein, unknown function	NA
49	PF3D7_0416000	Pf3D7_04_v3	701526	-	2637	-0.691	-1.273	-0.108	6.293	-2.845	7.24e-03	9.09e-02	-2.692	RNA-binding protein, putative	NA
26	PF3D7_0303400	Pf3D7_03_v3	178420	+	2708	1.000	0.628	1.372	1.354	2.833	7.46e-03	9.26e-02	-2.422	palmitoyltransferase DHHC1	DHHC1
158	PF3D7_0905300	Pf3D7_09_v3	251353	-	18357	-0.896	-1.244	-0.548	2.709	-2.834	7.44e-03	9.26e-02	-2.463	dynein heavy chain, putative	NA
208	PF3D7_1111000	Pf3D7_11_v3	434802	+	1740	0.564	-0.224	1.352	5.391	2.833	7.46e-03	9.26e-02	-2.639	tRNA m5C-methyltransferase, putative	NA
327	PF3D7_1423200	Pf3D7_14_v3	933059	+	2299	-0.588	-0.881	-0.294	5.853	-2.834	7.45e-03	9.26e-02	-2.687	peptidyl-prolyl cis-trans isomerase	CYP52
74	PF3D7_0523300	Pf3D7_05_v3	970266	-	697	1.001	0.197	1.805	0.700	2.826	7.59e-03	9.29e-02	-2.430	conserved Plasmodium protein, unknown function	NA
176	PF3D7_1002300	Pf3D7_10_v3	117242	+	1293	0.867	0.028	1.706	1.347	2.827	7.58e-03	9.29e-02	-2.436	conserved Plasmodium protein, unknown function	NA
290	PF3D7_1322100	Pf3D7_13_v3	920971	+	8479	-0.528	-1.188	0.132	9.385	-2.826	7.59e-03	9.29e-02	-2.877	histone-lysine N-methyltransferase SET2	SET2
294	PF3D7_1341100	Pf3D7_13_v3	1632602	-	108	-1.102	-1.788	-0.415	3.017	-2.826	7.60e-03	9.29e-02	-2.474	U6 spliceosomal RNA	NA
314	PF3D7_1373500	Pf3D7_13_v3	2884786	-	7555	-0.781	-1.245	-0.318	4.450	-2.826	7.60e-03	9.29e-02	-2.568	erythrocyte membrane protein 1, PfEMP1	VAR
245	PF3D7_1225200	Pf3D7_12_v3	1024455	-	3564	0.382	-0.352	1.116	6.893	2.824	7.64e-03	9.32e-02	-2.789	conserved Plasmodium protein, unknown function	NA
63	PF3D7_0506700	Pf3D7_05_v3	280886	+	2460	-0.562	-1.252	0.128	4.982	-2.815	7.81e-03	9.49e-02	-2.656	GTPase-activating protein, putative	NA
219	PF3D7_1126100	Pf3D7_11_v3	1018366	-	4130	0.858	0.339	1.377	1.600	2.811	7.90e-03	9.57e-02	-2.473	autophagy-related protein 7, putative	ATG7
88	PF3D7_0607000	Pf3D7_06_v3	293864	+	2934	-0.447	-1.635	0.742	10.481	-2.807	7.97e-03	9.61e-02	-2.942	translation initiation factor IF-2, putative	NA
94	PF3D7_0614200	Pf3D7_06_v3	593172	-	2733	0.813	-0.615	2.241	3.914	2.807	7.98e-03	9.61e-02	-2.578	cytosolic Fe-S cluster assembly factor NAR1, putative	NAR1
140	PF3D7_0808600	Pf3D7_08_v3	431165	+	7887	-0.842	-1.341	-0.344	4.353	-2.804	8.04e-03	9.66e-02	-2.618	erythrocyte membrane protein 1, PfEMP1	VAR
126	PF3D7_0717400	Pf3D7_07_v3	751877	+	2256	-0.411	-1.105	0.283	7.621	-2.802	8.08e-03	9.67e-02	-2.882	queuine tRNA-ribosyltransferase, putative	NA
332	PF3D7_1431600	Pf3D7_14_v3	1244018	+	1389	1.118	0.219	2.016	1.156	2.798	8.15e-03	9.74e-02	-2.492	succinyl-CoA ligase [ADP-forming] subunit beta, putative	NA
38	PF3D7_0400200	Pf3D7_04_v3	38955	+	1200	-1.094	-1.337	-0.852	2.992	-2.789	8.34e-03	9.86e-02	-2.559	erythrocyte membrane protein 1 (PfEMP1), exon 2, pseudogene	NA
89	PF3D7_0608700	Pf3D7_06_v3	358391	+	1813	-0.362	-0.916	0.193	9.108	-2.789	8.35e-03	9.86e-02	-2.970	T-complex protein 1 subunit zeta	CCT6
344	PF3D7_1450300	Pf3D7_14_v3	2056641	+	2598	0.766	0.095	1.436	5.175	2.789	8.35e-03	9.86e-02	-2.736	NADPH–cytochrome P450 reductase, putative	CPR
351	PF3D7_1459300	Pf3D7_14_v3	2432177	+	570	0.803	0.428	1.178	1.803	2.789	8.35e-03	9.86e-02	-2.526	OPA3-like protein, putative	NA
320	PF3D7_1412700	Pf3D7_14_v3	512363	+	3660	-0.569	-1.258	0.119	5.935	-2.787	8.40e-03	9.89e-02	-2.794	AAA family ATPase, putative	NA
113	PF3D7_0707900	Pf3D7_07_v3	366929	+	780	-0.414	-1.143	0.315	7.553	-2.784	8.46e-03	9.90e-02	-2.921	ribosomal protein S8e, putative	NA
261	PF3D7_1244100	Pf3D7_12_v3	1847677	+	4480	-0.482	-0.753	-0.210	5.912	-2.781	8.53e-03	9.90e-02	-2.809	N-alpha-acetyltransferase 15, NatA auxiliary subunit, putative	NA
321	PF3D7_1414100	Pf3D7_14_v3	560093	+	2232	0.548	-0.272	1.368	6.992	2.781	8.51e-03	9.90e-02	-2.891	conserved Plasmodium protein, unknown function	NA
336	PF3D7_1439100	Pf3D7_14_v3	1580750	+	8108	-0.574	-0.972	-0.177	6.512	-2.782	8.50e-03	9.90e-02	-2.857	DEAD/DEAH box helicase, putative	NA
342	PF3D7_1447200	Pf3D7_14_v3	1933985	+	1791	-0.429	-0.856	-0.001	7.819	-2.781	8.52e-03	9.90e-02	-2.944	conserved Plasmodium protein, unknown function	NA
253	PF3D7_1232200	Pf3D7_12_v3	1333134	+	1763	-0.941	-1.961	0.079	0.865	-2.777	8.60e-03	9.95e-02	-2.533	dihydrolipoyl dehydrogenase, mitochondrial	LPD1

Heatmap of deregulated genes

col_annot <- data.frame(row.names = colnames(v$E), stringsAsFactors = F)
col_annot$phenotype[substring(colnames(v$E), 1, 1) == "I"] <- "non-severe"
col_annot$phenotype[substring(colnames(v$E), 1, 1) == "S"] <- "severe"
col_annot$phenotype <- as.factor(col_annot$phenotype)

pheatmap(v2$E[rownames(v$E) %in% top_ring_ruv$GeneID, ], show_rownames = FALSE, scale = "row", annotation_col = col_annot, annotation_colors = list(phenotype = c(`non-severe` = colors[1], 
    severe = colors[2])))

Gene set analysis

First GO set enrichment using limma’s mroast.

# genesets <- AnnotationDbi::select(org.Pf.plasmo.db, keys=top_ring_ruv$GeneID, keytype='ALIAS', columns = c('GO','PATH')) go.gene.sets <-
# lapply(split.data.frame(genesets,genesets$GO), function(x) as.vector(x$ALIAS)) kegg.gene.sets <- lapply(split.data.frame(genesets,genesets$PATH),
# function(x) as.vector(x$ALIAS))
MIN_SET_SIZE <- 3

go.gene.df <- fread("./data/go_gene_lists.txt", sep = "\t", data.table = FALSE)
go.gene.sets <- lapply(go.gene.df$Genes, function(x) {
    x <- unlist(str_split(x, ","))
    x <- x[x != ""]
})
names(go.gene.sets) <- go.gene.df$GO_ID
go.gene.sets <- go.gene.sets[unlist(lapply(go.gene.sets, length)) >= MIN_SET_SIZE]

kegg.gene.df <- fread("./data/kegg_gene_lists.txt", sep = "\t", data.table = FALSE)
kegg.gene.sets <- lapply(kegg.gene.df$Genes, function(x) {
    x <- unlist(str_split(x, ","))
    x <- x[x != ""]
})
names(kegg.gene.sets) <- kegg.gene.df$KEGG_ID
kegg.gene.sets <- kegg.gene.sets[unlist(lapply(kegg.gene.sets, length)) >= MIN_SET_SIZE]

indices <- ids2indices(go.gene.sets, rownames(v2), remove.empty = TRUE)
go_mr <- mroast(v2, index = indices, design = modRUV, contrast = 2, nrot = 10000, set.statistic = "floormean")
go_cam <- camera(v2, index = indices, design = modRUV, contrast = 2)
kable(go_mr, digits = 3)

	NGenes	PropDown	PropUp	Direction	PValue	FDR	PValue.Mixed	FDR.Mixed
GO:0016337	54	0.852	0.019	Down	0.000	0.001	0.000	0.001
GO:0098602	54	0.852	0.019	Down	0.000	0.001	0.000	0.001
GO:0007155	69	0.696	0.014	Down	0.000	0.001	0.000	0.001
GO:0020035	93	0.634	0.032	Down	0.000	0.001	0.000	0.001
GO:0044406	93	0.634	0.032	Down	0.000	0.001	0.000	0.001
GO:0034118	87	0.632	0.011	Down	0.000	0.001	0.000	0.001
GO:0020013	87	0.632	0.011	Down	0.000	0.001	0.000	0.001
GO:0030155	87	0.632	0.011	Down	0.000	0.001	0.000	0.001
GO:0034110	87	0.632	0.011	Down	0.000	0.001	0.000	0.001
GO:0022407	87	0.632	0.011	Down	0.000	0.001	0.000	0.001
GO:0044068	88	0.625	0.011	Down	0.000	0.001	0.000	0.001
GO:0051807	93	0.624	0.022	Down	0.000	0.001	0.000	0.001
GO:0051834	93	0.624	0.022	Down	0.000	0.001	0.000	0.001
GO:0051832	93	0.624	0.022	Down	0.000	0.001	0.000	0.001
GO:0043207	93	0.624	0.022	Down	0.000	0.001	0.000	0.001
GO:0052564	93	0.624	0.022	Down	0.000	0.001	0.000	0.001
GO:0051805	93	0.624	0.022	Down	0.000	0.001	0.000	0.001
GO:0052173	93	0.624	0.022	Down	0.000	0.001	0.000	0.003
GO:0051809	92	0.620	0.022	Down	0.000	0.001	0.000	0.001
GO:0020033	92	0.620	0.022	Down	0.000	0.001	0.000	0.001
GO:0044003	89	0.618	0.011	Down	0.000	0.001	0.000	0.001
GO:0051817	89	0.618	0.011	Down	0.000	0.001	0.000	0.001
GO:0009607	94	0.617	0.021	Down	0.000	0.001	0.000	0.001
GO:0035821	90	0.611	0.022	Down	0.000	0.001	0.000	0.001
GO:0009605	100	0.610	0.030	Down	0.000	0.001	0.000	0.001
GO:0022610	113	0.558	0.035	Down	0.000	0.001	0.000	0.001
GO:0065008	149	0.456	0.107	Down	0.000	0.001	0.000	0.001
GO:0044403	157	0.446	0.096	Down	0.000	0.001	0.000	0.001
GO:0044419	157	0.446	0.096	Down	0.000	0.001	0.000	0.001
GO:0051701	147	0.442	0.082	Down	0.000	0.001	0.000	0.001
GO:0050896	291	0.357	0.096	Down	0.000	0.001	0.000	0.001
GO:0065007	401	0.309	0.150	Down	0.000	0.001	0.000	0.001
GO:0050794	359	0.309	0.142	Down	0.000	0.001	0.000	0.001
GO:0009405	84	0.690	0.048	Down	0.000	0.004	0.000	0.003
GO:0051704	189	0.444	0.095	Down	0.000	0.004	0.000	0.003
GO:0050789	380	0.321	0.139	Down	0.000	0.004	0.000	0.001
GO:0051707	93	0.624	0.022	Down	0.000	0.006	0.000	0.003
GO:0009396	4	0.500	0.000	Down	0.000	0.006	0.002	0.008
GO:0016579	11	0.545	0.182	Down	0.000	0.008	0.001	0.006
GO:0006848	2	0.500	0.000	Down	0.000	0.008	0.001	0.006
GO:0000245	9	0.667	0.111	Down	0.000	0.010	0.000	0.003
GO:0070646	11	0.545	0.182	Down	0.000	0.010	0.001	0.006
GO:0006760	5	0.400	0.200	Down	0.000	0.010	0.000	0.006
GO:0031123	8	0.125	0.750	Up	0.001	0.012	0.001	0.006
GO:0016485	10	0.500	0.000	Down	0.001	0.014	0.002	0.009
GO:0031167	2	1.000	0.000	Down	0.001	0.016	0.001	0.006
GO:0042026	3	0.667	0.000	Down	0.001	0.017	0.001	0.008
GO:0051604	12	0.417	0.000	Down	0.001	0.017	0.004	0.013
GO:0008154	1	1.000	0.000	Down	0.001	0.017	0.001	0.007
GO:0006206	6	0.500	0.000	Down	0.001	0.017	0.004	0.014
GO:0009112	7	0.429	0.000	Down	0.001	0.017	0.005	0.015
GO:0019220	27	0.222	0.407	Up	0.001	0.017	0.000	0.001
GO:0006950	91	0.286	0.165	Down	0.001	0.017	0.000	0.005
GO:0006207	5	0.400	0.000	Down	0.001	0.022	0.012	0.026
GO:0046112	5	0.400	0.000	Down	0.001	0.025	0.013	0.028
GO:0048519	16	0.312	0.375	Down	0.001	0.025	0.000	0.004
GO:0044699	809	0.235	0.178	Down	0.001	0.025	0.000	0.006
GO:0006457	72	0.417	0.097	Down	0.002	0.025	0.001	0.006
GO:0019856	5	0.400	0.000	Down	0.002	0.025	0.014	0.029
GO:0007007	3	0.667	0.000	Down	0.002	0.027	0.005	0.015
GO:0090151	3	0.667	0.000	Down	0.002	0.027	0.006	0.016
GO:0071840	251	0.283	0.151	Down	0.002	0.027	0.001	0.007
GO:0045039	3	0.667	0.000	Down	0.002	0.028	0.006	0.016
GO:0051174	27	0.222	0.407	Up	0.002	0.028	0.000	0.006
GO:0042325	5	0.000	0.800	Up	0.002	0.028	0.010	0.022
GO:0043631	6	0.167	0.667	Up	0.002	0.028	0.002	0.009
GO:0007006	3	0.667	0.000	Down	0.002	0.029	0.005	0.015
GO:0006518	11	0.364	0.182	Down	0.002	0.030	0.003	0.011
GO:0009260	18	0.111	0.333	Up	0.002	0.030	0.002	0.009
GO:0001817	3	0.667	0.000	Down	0.002	0.031	0.002	0.010
GO:0006730	4	0.500	0.250	Down	0.002	0.031	0.001	0.006
GO:0006575	13	0.308	0.308	Down	0.002	0.031	0.001	0.006
GO:0016568	18	0.389	0.167	Down	0.002	0.032	0.001	0.007
GO:0016571	5	0.600	0.000	Down	0.003	0.034	0.002	0.010
GO:0001932	5	0.000	0.800	Up	0.003	0.034	0.010	0.022
GO:0031399	5	0.000	0.800	Up	0.003	0.034	0.010	0.023
GO:0002098	4	0.000	0.500	Up	0.003	0.034	0.011	0.024
GO:0008033	37	0.108	0.351	Up	0.003	0.035	0.001	0.007
GO:0015914	4	0.250	0.250	Down	0.003	0.035	0.000	0.001
GO:0042221	68	0.250	0.088	Down	0.003	0.036	0.002	0.008
GO:0009152	17	0.118	0.353	Up	0.003	0.036	0.002	0.009
GO:0044085	153	0.301	0.150	Down	0.003	0.037	0.001	0.007
GO:0051239	3	0.667	0.000	Down	0.003	0.037	0.003	0.012
GO:0009201	8	0.125	0.625	Up	0.003	0.037	0.002	0.010
GO:1902580	33	0.273	0.061	Down	0.003	0.037	0.007	0.018
GO:1901137	55	0.145	0.327	Up	0.003	0.037	0.001	0.006
GO:0009206	8	0.125	0.625	Up	0.004	0.037	0.002	0.010
GO:0006378	5	0.200	0.600	Up	0.004	0.037	0.003	0.010
GO:0050790	27	0.259	0.370	Up	0.004	0.037	0.001	0.006
GO:0006325	29	0.345	0.172	Down	0.004	0.037	0.001	0.008
GO:0006281	50	0.160	0.220	Up	0.004	0.037	0.003	0.011
GO:0033554	55	0.200	0.200	Up	0.004	0.037	0.002	0.009
GO:0009628	22	0.500	0.091	Down	0.004	0.037	0.002	0.009
GO:0043603	15	0.267	0.133	Down	0.004	0.037	0.014	0.028
GO:0006996	110	0.264	0.145	Down	0.004	0.037	0.002	0.009
GO:0034641	602	0.236	0.199	Down	0.004	0.037	0.000	0.006
GO:0044260	985	0.236	0.196	Down	0.004	0.037	0.001	0.006
GO:0070585	14	0.500	0.071	Down	0.004	0.037	0.004	0.013
GO:0007005	14	0.500	0.071	Down	0.004	0.037	0.004	0.013
GO:0071806	16	0.312	0.062	Down	0.004	0.037	0.008	0.019
GO:0006396	207	0.295	0.242	Down	0.004	0.037	0.000	0.005
GO:0009987	1474	0.224	0.190	Down	0.004	0.037	0.001	0.006
GO:0072594	32	0.281	0.062	Down	0.004	0.037	0.007	0.018
GO:0044238	1268	0.226	0.189	Down	0.004	0.037	0.000	0.006
GO:0043414	18	0.278	0.278	Down	0.004	0.037	0.001	0.006
GO:0016043	183	0.273	0.148	Down	0.004	0.037	0.001	0.008
GO:0016070	365	0.266	0.227	Down	0.004	0.037	0.001	0.006
GO:0008380	81	0.407	0.173	Down	0.004	0.037	0.001	0.006
GO:0042559	6	0.333	0.333	Down	0.004	0.037	0.001	0.008
GO:0006725	583	0.233	0.201	Down	0.004	0.037	0.000	0.006
GO:0046483	584	0.233	0.202	Down	0.004	0.037	0.000	0.005
GO:0031124	5	0.200	0.600	Up	0.004	0.037	0.003	0.011
GO:1901360	587	0.232	0.201	Down	0.004	0.037	0.000	0.003
GO:0006807	627	0.230	0.203	Down	0.004	0.037	0.001	0.006
GO:0043933	107	0.290	0.140	Down	0.005	0.037	0.001	0.006
GO:0010467	524	0.258	0.200	Down	0.005	0.037	0.000	0.005
GO:0043170	1043	0.232	0.196	Down	0.005	0.037	0.001	0.006
GO:0009266	21	0.476	0.095	Down	0.005	0.037	0.002	0.009
GO:0065009	27	0.259	0.370	Up	0.005	0.037	0.001	0.006
GO:0046390	19	0.105	0.316	Up	0.005	0.037	0.005	0.015
GO:0006139	560	0.238	0.196	Down	0.005	0.037	0.000	0.004
GO:0006094	5	0.800	0.000	Down	0.005	0.037	0.005	0.015
GO:0042398	11	0.273	0.273	Down	0.005	0.037	0.002	0.010
GO:0051276	43	0.326	0.140	Down	0.005	0.037	0.005	0.014
GO:0033365	33	0.273	0.091	Down	0.005	0.037	0.007	0.017
GO:0072655	14	0.500	0.071	Down	0.005	0.037	0.005	0.015
GO:0006626	14	0.500	0.071	Down	0.005	0.037	0.005	0.015
GO:0072657	11	0.273	0.091	Down	0.005	0.037	0.005	0.015
GO:0090304	471	0.246	0.210	Down	0.005	0.037	0.001	0.006
GO:0006974	51	0.176	0.216	Up	0.005	0.037	0.004	0.013
GO:0045454	29	0.345	0.207	Down	0.005	0.037	0.000	0.004
GO:0002097	4	0.000	0.500	Up	0.005	0.038	0.011	0.024
GO:0046364	6	0.667	0.000	Down	0.005	0.038	0.007	0.017
GO:0016255	4	0.000	1.000	Up	0.005	0.038	0.006	0.017
GO:0019319	6	0.667	0.000	Down	0.005	0.038	0.006	0.017
GO:0006605	34	0.265	0.059	Down	0.005	0.038	0.009	0.021
GO:0031338	14	0.000	0.357	Up	0.005	0.038	0.003	0.012
GO:0071704	1299	0.221	0.193	Down	0.006	0.039	0.001	0.006
GO:0051188	30	0.067	0.333	Up	0.006	0.039	0.002	0.010
GO:0006520	75	0.280	0.200	Down	0.006	0.039	0.001	0.008
GO:0090150	11	0.273	0.091	Down	0.006	0.039	0.006	0.016
GO:0009408	20	0.450	0.100	Down	0.006	0.039	0.002	0.009
GO:0019222	152	0.243	0.184	Down	0.006	0.039	0.003	0.011
GO:0006813	4	0.000	0.500	Up	0.006	0.039	0.019	0.036
GO:0008213	8	0.375	0.250	Down	0.006	0.039	0.001	0.008
GO:0016071	100	0.310	0.240	Down	0.006	0.039	0.001	0.006
GO:0035966	12	0.417	0.083	Down	0.006	0.039	0.003	0.011
GO:0008152	1383	0.221	0.195	Down	0.006	0.039	0.001	0.006
GO:0006479	8	0.375	0.250	Down	0.006	0.039	0.002	0.009
GO:0033124	18	0.222	0.333	Up	0.006	0.039	0.001	0.006
GO:0032012	3	0.333	0.667	Up	0.006	0.039	0.001	0.007
GO:0006164	19	0.105	0.316	Up	0.006	0.039	0.002	0.009
GO:0044237	1238	0.226	0.193	Down	0.006	0.039	0.001	0.006
GO:0010608	25	0.360	0.080	Down	0.006	0.039	0.005	0.014
GO:0032312	2	0.000	1.000	Up	0.006	0.039	0.006	0.017
GO:0032259	26	0.269	0.231	Down	0.006	0.039	0.000	0.003
GO:0009145	9	0.222	0.556	Up	0.006	0.040	0.000	0.005
GO:0043087	18	0.222	0.333	Up	0.007	0.040	0.001	0.007
GO:0051051	3	0.000	1.000	Up	0.007	0.040	0.007	0.018
GO:0006271	5	0.000	0.600	Up	0.007	0.040	0.017	0.033
GO:0042493	51	0.235	0.078	Down	0.007	0.040	0.002	0.010
GO:0006265	3	0.667	0.333	Down	0.007	0.041	0.002	0.008
GO:0000154	5	0.600	0.000	Down	0.007	0.042	0.004	0.014
GO:0019752	129	0.279	0.178	Down	0.007	0.042	0.002	0.010
GO:0009894	22	0.364	0.273	Down	0.007	0.042	0.001	0.006
GO:1901564	179	0.246	0.201	Down	0.007	0.042	0.001	0.006
GO:0019538	628	0.231	0.182	Down	0.007	0.042	0.001	0.006
GO:0030029	10	0.300	0.200	Down	0.007	0.043	0.004	0.014
GO:0006986	12	0.417	0.083	Down	0.008	0.043	0.003	0.012
GO:0000377	59	0.407	0.186	Down	0.008	0.043	0.001	0.006
GO:0042451	17	0.176	0.353	Up	0.008	0.043	0.001	0.007
GO:0010033	13	0.385	0.077	Down	0.008	0.043	0.003	0.012
GO:0043436	130	0.277	0.177	Down	0.008	0.043	0.002	0.009
GO:0044724	24	0.583	0.042	Down	0.008	0.043	0.008	0.019
GO:0000375	64	0.422	0.172	Down	0.008	0.043	0.001	0.007
GO:0000398	59	0.407	0.186	Down	0.008	0.044	0.001	0.006
GO:0006397	93	0.323	0.258	Down	0.008	0.044	0.001	0.006
GO:0034968	4	0.500	0.000	Down	0.008	0.044	0.006	0.017
GO:0080090	141	0.234	0.184	Down	0.008	0.044	0.002	0.010
GO:0000079	3	0.000	1.000	Up	0.008	0.044	0.009	0.020
GO:0046129	17	0.176	0.353	Up	0.008	0.044	0.001	0.007
GO:0006096	17	0.647	0.059	Down	0.008	0.044	0.008	0.019
GO:0009247	12	0.083	0.583	Up	0.009	0.045	0.010	0.023
GO:0051336	21	0.286	0.333	Up	0.009	0.045	0.000	0.003
GO:0030036	8	0.250	0.250	Down	0.009	0.045	0.005	0.015
GO:0006338	4	0.500	0.000	Down	0.009	0.045	0.013	0.028
GO:0006140	19	0.263	0.316	Up	0.009	0.045	0.001	0.006
GO:0016052	24	0.583	0.042	Down	0.009	0.045	0.009	0.022
GO:0000910	4	0.000	0.500	Up	0.009	0.045	0.019	0.036
GO:0006081	6	0.167	0.333	Up	0.009	0.045	0.006	0.017
GO:0016051	12	0.500	0.000	Down	0.009	0.045	0.008	0.019
GO:0030811	19	0.263	0.316	Up	0.009	0.045	0.001	0.007
GO:0006790	20	0.100	0.300	Up	0.009	0.045	0.009	0.022
GO:0033121	19	0.263	0.316	Up	0.009	0.045	0.001	0.006
GO:0034660	124	0.266	0.234	Down	0.009	0.045	0.001	0.006
GO:0043412	249	0.157	0.225	Up	0.009	0.045	0.001	0.007
GO:0006475	4	0.000	0.750	Up	0.009	0.045	0.033	0.053
GO:0009118	19	0.263	0.316	Up	0.009	0.045	0.000	0.006
GO:0022616	5	0.000	0.600	Up	0.009	0.045	0.021	0.039
GO:0051651	2	0.000	1.000	Up	0.010	0.045	0.010	0.022
GO:0006082	130	0.277	0.177	Down	0.010	0.045	0.003	0.011
GO:1900542	19	0.263	0.316	Up	0.010	0.045	0.001	0.006
GO:1901607	11	0.182	0.091	Down	0.010	0.045	0.021	0.038
GO:0018393	4	0.000	0.750	Up	0.010	0.045	0.033	0.053
GO:0009452	6	0.333	0.167	Down	0.010	0.045	0.002	0.010
GO:0022613	98	0.327	0.143	Down	0.010	0.045	0.002	0.010
GO:0071900	3	0.000	1.000	Up	0.010	0.045	0.010	0.023
GO:0006379	4	0.250	0.750	Up	0.010	0.045	0.007	0.018
GO:0046467	13	0.077	0.615	Up	0.010	0.045	0.010	0.023
GO:0006465	7	0.429	0.000	Down	0.010	0.045	0.024	0.043
GO:0009108	24	0.083	0.292	Up	0.010	0.045	0.002	0.009
GO:0016573	4	0.000	0.750	Up	0.010	0.046	0.033	0.053
GO:0044743	6	0.667	0.000	Down	0.010	0.046	0.009	0.020
GO:0042558	7	0.286	0.429	Down	0.010	0.046	0.001	0.008
GO:0010468	116	0.224	0.147	Down	0.010	0.046	0.006	0.016
GO:0048523	10	0.300	0.200	Down	0.010	0.046	0.007	0.018
GO:0006754	7	0.143	0.571	Up	0.010	0.046	0.007	0.018
GO:0034622	64	0.328	0.141	Down	0.010	0.046	0.003	0.011
GO:0031329	19	0.263	0.316	Up	0.010	0.046	0.001	0.006
GO:0006410	5	0.000	0.600	Up	0.011	0.046	0.021	0.038
GO:0044712	59	0.339	0.136	Down	0.011	0.046	0.004	0.013
GO:0006399	78	0.231	0.269	Up	0.011	0.046	0.002	0.008
GO:0032507	2	0.000	1.000	Up	0.011	0.046	0.011	0.024
GO:0036260	6	0.333	0.167	Down	0.011	0.046	0.002	0.009
GO:0008616	4	0.500	0.250	Down	0.011	0.046	0.005	0.014
GO:0046116	4	0.500	0.250	Down	0.011	0.046	0.006	0.016
GO:0033043	19	0.053	0.316	Up	0.011	0.046	0.004	0.013
GO:0060255	128	0.234	0.164	Down	0.011	0.046	0.004	0.013
GO:0006090	24	0.458	0.167	Down	0.011	0.047	0.004	0.014
GO:0018394	4	0.000	0.750	Up	0.011	0.047	0.033	0.053
GO:0006006	12	0.583	0.000	Down	0.011	0.047	0.013	0.027
GO:0006289	11	0.182	0.364	Up	0.011	0.047	0.001	0.006
GO:0044267	562	0.237	0.181	Down	0.011	0.047	0.002	0.008
GO:0010629	6	0.500	0.167	Down	0.011	0.047	0.003	0.011
GO:0042158	18	0.000	0.556	Up	0.012	0.048	0.013	0.028
GO:0043241	6	0.000	0.500	Up	0.012	0.048	0.062	0.083
GO:0044271	158	0.196	0.215	Up	0.012	0.049	0.000	0.005
GO:0042176	3	1.000	0.000	Down	0.012	0.049	0.012	0.026
GO:0065003	74	0.297	0.135	Down	0.012	0.049	0.002	0.010
GO:0016072	48	0.312	0.188	Down	0.012	0.049	0.002	0.009
GO:0006497	18	0.000	0.556	Up	0.012	0.049	0.013	0.028
GO:0042157	18	0.000	0.556	Up	0.012	0.049	0.013	0.028
GO:0045017	17	0.059	0.471	Up	0.012	0.049	0.007	0.018
GO:0043543	15	0.000	0.467	Up	0.012	0.049	0.034	0.053
GO:0045859	4	0.000	0.750	Up	0.013	0.049	0.020	0.037
GO:0051186	45	0.156	0.267	Up	0.013	0.049	0.001	0.006
GO:0043549	4	0.000	0.750	Up	0.013	0.049	0.019	0.036
GO:0022607	83	0.289	0.145	Down	0.013	0.049	0.002	0.009
GO:0006413	48	0.208	0.167	Down	0.013	0.049	0.007	0.018
GO:0031323	139	0.216	0.194	Down	0.013	0.049	0.002	0.010
GO:0006664	13	0.077	0.538	Up	0.013	0.049	0.015	0.030
GO:0035383	7	0.000	0.429	Up	0.013	0.049	0.017	0.032
GO:0009892	8	0.375	0.250	Down	0.013	0.049	0.001	0.008
GO:0043648	10	0.300	0.000	Down	0.013	0.049	0.038	0.057
GO:0006259	120	0.175	0.192	Up	0.013	0.050	0.001	0.007
GO:0090305	10	0.200	0.500	Up	0.013	0.050	0.004	0.013
GO:0007275	6	0.000	0.333	Up	0.013	0.050	0.016	0.032
GO:0007018	19	0.263	0.211	Down	0.013	0.050	0.001	0.006
GO:0015985	7	0.143	0.571	Up	0.013	0.050	0.009	0.021
GO:0006364	48	0.312	0.188	Down	0.013	0.050	0.002	0.009
GO:0015986	7	0.143	0.571	Up	0.014	0.050	0.009	0.021
GO:0065002	11	0.364	0.000	Down	0.014	0.050	0.020	0.037
GO:0019725	42	0.262	0.238	Up	0.014	0.051	0.000	0.006
GO:0006417	22	0.318	0.091	Down	0.014	0.052	0.008	0.020
GO:0044092	3	0.667	0.333	Down	0.014	0.052	0.001	0.007
GO:0043086	3	0.667	0.333	Down	0.014	0.052	0.001	0.007
GO:0071826	31	0.323	0.097	Down	0.014	0.052	0.014	0.028
GO:0044707	7	0.000	0.286	Up	0.014	0.052	0.026	0.045
GO:0006875	4	0.250	0.750	Up	0.014	0.052	0.002	0.009
GO:0019318	14	0.500	0.000	Down	0.015	0.052	0.019	0.036
GO:0032318	15	0.200	0.333	Up	0.015	0.052	0.002	0.010
GO:0051338	4	0.000	0.750	Up	0.015	0.053	0.020	0.037
GO:0090501	4	0.250	0.500	Down	0.015	0.053	0.002	0.008
GO:0006839	18	0.389	0.056	Down	0.015	0.053	0.015	0.030
GO:0006643	15	0.067	0.600	Up	0.015	0.053	0.014	0.029
GO:0051246	31	0.355	0.194	Down	0.015	0.053	0.004	0.014
GO:1902531	17	0.294	0.294	Down	0.015	0.053	0.001	0.006
GO:0044763	585	0.200	0.191	Up	0.015	0.054	0.000	0.006
GO:0042455	22	0.227	0.318	Up	0.016	0.054	0.000	0.005
GO:0006066	7	0.286	0.000	Down	0.016	0.054	0.045	0.064
GO:0046474	16	0.062	0.500	Up	0.016	0.054	0.008	0.020
GO:0010605	7	0.429	0.286	Down	0.016	0.054	0.001	0.007
GO:1901605	24	0.167	0.167	Down	0.016	0.054	0.006	0.016
GO:0006637	7	0.000	0.429	Up	0.016	0.054	0.018	0.035
GO:0034654	128	0.211	0.188	Down	0.016	0.054	0.001	0.007
GO:0018130	152	0.204	0.204	Down	0.016	0.054	0.001	0.006
GO:0051716	109	0.174	0.156	Up	0.016	0.054	0.002	0.010
GO:0006732	37	0.189	0.243	Up	0.016	0.054	0.000	0.006
GO:0006812	42	0.214	0.262	Up	0.016	0.054	0.001	0.006
GO:0007049	36	0.083	0.167	Up	0.016	0.054	0.020	0.037
GO:0006506	9	0.000	0.667	Up	0.016	0.054	0.016	0.032
GO:0005996	14	0.500	0.000	Down	0.017	0.054	0.019	0.036
GO:0044272	14	0.071	0.357	Up	0.017	0.054	0.022	0.039
GO:0046578	17	0.294	0.294	Down	0.017	0.054	0.000	0.004
GO:0044767	11	0.000	0.273	Up	0.017	0.054	0.019	0.036
GO:0044723	42	0.429	0.071	Down	0.017	0.054	0.008	0.019
GO:0009142	10	0.200	0.500	Up	0.017	0.054	0.002	0.010
GO:0032501	8	0.000	0.250	Up	0.017	0.054	0.040	0.060
GO:0048518	11	0.364	0.091	Down	0.017	0.054	0.010	0.023
GO:0009163	22	0.227	0.318	Up	0.017	0.054	0.000	0.005
GO:0070647	29	0.310	0.172	Down	0.017	0.054	0.002	0.009
GO:0071976	4	0.000	0.250	Up	0.017	0.055	0.057	0.078
GO:0006897	7	0.286	0.143	Down	0.017	0.055	0.004	0.012
GO:0009451	43	0.140	0.233	Up	0.017	0.055	0.001	0.006
GO:0055065	4	0.250	0.750	Up	0.017	0.055	0.002	0.009
GO:0009889	111	0.207	0.153	Down	0.017	0.055	0.005	0.015
GO:0044281	231	0.242	0.169	Down	0.017	0.055	0.002	0.009
GO:0009058	529	0.189	0.208	Up	0.018	0.055	0.001	0.007
GO:0051056	17	0.294	0.294	Down	0.018	0.055	0.001	0.006
GO:0046148	6	0.000	0.500	Up	0.018	0.056	0.050	0.069
GO:0044249	516	0.186	0.205	Up	0.018	0.056	0.001	0.008
GO:0031326	111	0.207	0.153	Down	0.018	0.056	0.006	0.017
GO:1901362	155	0.200	0.200	Down	0.018	0.056	0.000	0.005
GO:0006779	6	0.000	0.500	Up	0.018	0.056	0.047	0.066
GO:0016042	5	0.200	0.400	Up	0.019	0.056	0.001	0.006
GO:0032879	27	0.111	0.333	Up	0.019	0.056	0.002	0.009
GO:0030001	16	0.188	0.312	Up	0.019	0.056	0.004	0.014
GO:0045892	4	0.500	0.000	Down	0.019	0.056	0.029	0.048
GO:0005975	53	0.377	0.094	Down	0.019	0.056	0.006	0.017
GO:0072522	22	0.182	0.273	Up	0.019	0.056	0.002	0.009
GO:0000350	3	0.667	0.333	Down	0.019	0.057	0.008	0.019
GO:0006351	81	0.210	0.185	Down	0.019	0.057	0.002	0.009
GO:2000112	110	0.209	0.155	Down	0.019	0.057	0.007	0.018
GO:0051172	4	0.500	0.000	Down	0.019	0.057	0.027	0.047
GO:0051049	27	0.111	0.333	Up	0.019	0.057	0.001	0.008
GO:0032502	12	0.000	0.250	Up	0.019	0.057	0.024	0.043
GO:0051128	22	0.091	0.273	Up	0.020	0.057	0.002	0.009
GO:0019438	148	0.203	0.203	Up	0.020	0.057	0.001	0.006
GO:0044802	14	0.214	0.143	Down	0.020	0.058	0.005	0.015
GO:0033014	6	0.000	0.500	Up	0.020	0.058	0.051	0.071
GO:0009056	171	0.304	0.140	Down	0.020	0.058	0.003	0.011
GO:0006783	6	0.000	0.500	Up	0.020	0.058	0.048	0.068
GO:0045934	4	0.500	0.000	Down	0.020	0.058	0.028	0.047
GO:0010556	110	0.209	0.155	Down	0.020	0.058	0.005	0.015
GO:1901659	23	0.217	0.304	Up	0.020	0.058	0.000	0.004
GO:2000113	4	0.500	0.000	Down	0.020	0.058	0.028	0.048
GO:0001510	9	0.222	0.333	Up	0.020	0.058	0.000	0.003
GO:0051253	4	0.500	0.000	Down	0.021	0.059	0.026	0.045
GO:0032784	3	0.667	0.000	Down	0.021	0.059	0.023	0.042
GO:1902679	4	0.500	0.000	Down	0.021	0.059	0.028	0.048
GO:0048583	27	0.259	0.222	Down	0.021	0.059	0.000	0.006
GO:0045185	3	0.000	0.667	Up	0.021	0.059	0.016	0.032
GO:0061024	17	0.235	0.118	Down	0.021	0.059	0.010	0.023
GO:0042254	80	0.288	0.150	Down	0.021	0.059	0.004	0.013
GO:1901576	518	0.189	0.203	Up	0.021	0.059	0.001	0.007
GO:0006820	41	0.146	0.098	Down	0.021	0.060	0.029	0.049
GO:0006904	4	0.500	0.250	Down	0.022	0.061	0.000	0.001
GO:0009132	5	0.200	0.400	Up	0.022	0.061	0.001	0.006
GO:0010558	4	0.500	0.000	Down	0.022	0.062	0.029	0.048
GO:0022618	29	0.345	0.103	Down	0.023	0.062	0.014	0.028
GO:1901575	165	0.303	0.145	Down	0.023	0.062	0.003	0.012
GO:0007015	4	0.250	0.000	Down	0.023	0.063	0.030	0.049
GO:0006661	10	0.000	0.600	Up	0.023	0.063	0.023	0.041
GO:0006086	4	0.000	0.500	Up	0.023	0.063	0.033	0.053
GO:0048278	4	0.500	0.250	Down	0.023	0.063	0.000	0.003
GO:0031163	4	0.250	0.500	Up	0.023	0.063	0.004	0.013
GO:0022406	4	0.500	0.250	Down	0.024	0.064	0.000	0.003
GO:0006464	206	0.160	0.218	Up	0.024	0.064	0.001	0.008
GO:0051235	3	0.000	0.667	Up	0.024	0.064	0.016	0.031
GO:0016226	4	0.250	0.500	Up	0.024	0.064	0.004	0.012
GO:0035384	4	0.000	0.500	Up	0.024	0.064	0.032	0.053
GO:0009890	5	0.400	0.000	Down	0.024	0.064	0.032	0.052
GO:0006508	138	0.268	0.181	Down	0.025	0.066	0.001	0.008
GO:0035890	12	0.083	0.250	Up	0.025	0.066	0.058	0.079
GO:0036211	206	0.160	0.218	Up	0.025	0.066	0.001	0.008
GO:0044106	8	0.250	0.125	Down	0.025	0.066	0.013	0.027
GO:0006357	10	0.300	0.100	Down	0.026	0.067	0.016	0.032
GO:0006629	86	0.140	0.256	Up	0.026	0.067	0.004	0.014
GO:0006869	9	0.222	0.222	Down	0.026	0.067	0.010	0.023
GO:0032774	84	0.202	0.190	Down	0.026	0.068	0.001	0.008
GO:0031327	5	0.400	0.000	Down	0.026	0.068	0.035	0.054
GO:0019320	9	0.556	0.000	Down	0.026	0.068	0.027	0.047
GO:0043248	8	0.625	0.125	Down	0.026	0.068	0.019	0.036
GO:0006505	10	0.000	0.600	Up	0.026	0.068	0.025	0.045
GO:0006085	4	0.000	0.500	Up	0.026	0.068	0.036	0.055
GO:0018193	25	0.280	0.320	Up	0.026	0.068	0.000	0.004
GO:0006098	9	0.556	0.000	Down	0.026	0.068	0.028	0.047
GO:0009438	2	0.000	0.500	Up	0.027	0.068	0.005	0.015
GO:0032268	27	0.259	0.222	Down	0.027	0.068	0.005	0.014
GO:0042592	47	0.255	0.234	Up	0.027	0.068	0.001	0.007
GO:0010876	9	0.222	0.222	Down	0.027	0.068	0.008	0.019
GO:0070682	6	0.833	0.000	Down	0.027	0.068	0.027	0.047
GO:0050657	7	0.286	0.143	Down	0.027	0.069	0.034	0.054
GO:0034470	83	0.229	0.253	Down	0.028	0.069	0.002	0.009
GO:0046365	9	0.556	0.000	Down	0.028	0.069	0.026	0.045
GO:0044710	420	0.210	0.205	Down	0.028	0.069	0.001	0.007
GO:0006165	2	0.500	0.500	Up	0.028	0.070	0.002	0.009
GO:0050658	7	0.286	0.143	Down	0.028	0.070	0.033	0.053
GO:0006740	9	0.556	0.000	Down	0.028	0.070	0.027	0.047
GO:0046939	2	0.500	0.500	Up	0.029	0.070	0.002	0.010
GO:0010564	17	0.118	0.235	Up	0.029	0.070	0.036	0.056
GO:0051236	7	0.286	0.143	Down	0.029	0.070	0.035	0.054
GO:0009308	8	0.250	0.125	Down	0.029	0.070	0.014	0.029
GO:0051726	29	0.207	0.241	Up	0.029	0.070	0.006	0.016
GO:0006739	9	0.556	0.000	Down	0.029	0.070	0.029	0.049
GO:0006576	8	0.250	0.125	Down	0.029	0.070	0.014	0.028
GO:0044711	147	0.184	0.231	Up	0.029	0.071	0.001	0.006
GO:0032271	5	0.200	0.200	Down	0.029	0.071	0.068	0.090
GO:0042777	1	0.000	1.000	Up	0.030	0.071	0.030	0.049
GO:0006007	9	0.556	0.000	Down	0.030	0.071	0.029	0.048
GO:0019362	10	0.500	0.000	Down	0.030	0.071	0.038	0.057
GO:0006403	7	0.286	0.143	Down	0.030	0.071	0.039	0.058
GO:0046496	10	0.500	0.000	Down	0.030	0.071	0.040	0.060
GO:0044087	5	0.200	0.200	Down	0.030	0.071	0.067	0.089
GO:0032956	5	0.200	0.200	Down	0.030	0.072	0.068	0.089
GO:0008064	5	0.200	0.200	Down	0.030	0.072	0.064	0.085
GO:0030832	5	0.200	0.200	Down	0.030	0.072	0.067	0.089
GO:0006511	71	0.338	0.155	Down	0.030	0.072	0.004	0.013
GO:0090407	64	0.172	0.250	Up	0.031	0.072	0.002	0.009
GO:0071616	4	0.000	0.500	Up	0.031	0.072	0.040	0.060
GO:0015718	7	0.286	0.143	Down	0.031	0.074	0.009	0.022
GO:0006414	20	0.350	0.100	Down	0.032	0.074	0.015	0.030
GO:0033036	161	0.193	0.130	Down	0.032	0.074	0.005	0.015
GO:1901566	80	0.175	0.250	Up	0.032	0.074	0.000	0.005
GO:0030833	5	0.200	0.200	Down	0.032	0.074	0.068	0.090
GO:0043254	5	0.200	0.200	Down	0.032	0.074	0.069	0.090
GO:0016482	66	0.227	0.091	Down	0.032	0.075	0.013	0.028
GO:0006979	10	0.400	0.100	Down	0.033	0.075	0.027	0.047
GO:0032970	5	0.200	0.200	Down	0.033	0.075	0.070	0.091
GO:0007010	21	0.143	0.286	Up	0.033	0.075	0.005	0.015
GO:0051493	5	0.200	0.200	Down	0.033	0.075	0.070	0.091
GO:0032535	5	0.200	0.200	Down	0.033	0.075	0.074	0.095
GO:0008654	25	0.160	0.360	Up	0.033	0.075	0.005	0.015
GO:0051301	23	0.043	0.261	Up	0.033	0.076	0.024	0.043
GO:0018208	10	0.400	0.100	Down	0.033	0.076	0.006	0.016
GO:0000413	10	0.400	0.100	Down	0.034	0.076	0.005	0.015
GO:0006890	6	0.000	0.333	Up	0.034	0.076	0.041	0.060
GO:0006928	33	0.212	0.212	Down	0.034	0.076	0.002	0.010
GO:0006644	35	0.200	0.314	Up	0.034	0.076	0.002	0.010
GO:0009060	17	0.118	0.294	Up	0.034	0.076	0.020	0.037
GO:0008535	1	0.000	1.000	Up	0.034	0.077	0.034	0.054
GO:0035891	11	0.091	0.273	Up	0.034	0.077	0.066	0.088
GO:0008610	53	0.132	0.283	Up	0.035	0.077	0.012	0.026
GO:0090066	5	0.200	0.200	Down	0.035	0.077	0.070	0.091
GO:0019219	110	0.200	0.191	Down	0.035	0.077	0.003	0.011
GO:0051171	110	0.200	0.191	Down	0.035	0.078	0.003	0.011
GO:0044257	76	0.329	0.171	Down	0.036	0.079	0.005	0.014
GO:0006099	17	0.118	0.294	Up	0.036	0.079	0.019	0.036
GO:0051603	76	0.329	0.171	Down	0.036	0.080	0.005	0.014
GO:0043244	3	0.667	0.333	Down	0.036	0.080	0.012	0.027
GO:0044255	73	0.151	0.260	Up	0.037	0.080	0.007	0.018
GO:0006750	3	0.000	0.667	Up	0.037	0.080	0.039	0.058
GO:0043632	73	0.329	0.164	Down	0.037	0.080	0.006	0.015
GO:0009147	3	0.000	0.333	Up	0.037	0.081	0.053	0.073
GO:0097354	6	0.000	0.167	Up	0.037	0.081	0.170	0.199
GO:0043043	3	0.000	0.667	Up	0.037	0.081	0.040	0.059
GO:0018205	6	0.333	0.500	Up	0.037	0.081	0.011	0.024
GO:0031324	6	0.333	0.167	Down	0.037	0.081	0.014	0.029
GO:0034645	383	0.193	0.196	Down	0.038	0.081	0.003	0.011
GO:0019184	3	0.000	0.667	Up	0.038	0.082	0.036	0.055
GO:0015672	24	0.208	0.292	Up	0.038	0.082	0.002	0.010
GO:0019941	73	0.329	0.164	Down	0.039	0.084	0.006	0.016
GO:0018342	6	0.000	0.167	Up	0.040	0.084	0.168	0.198
GO:0016310	99	0.121	0.162	Up	0.040	0.084	0.008	0.019
GO:0006468	91	0.099	0.154	Up	0.040	0.084	0.013	0.028
GO:0007059	8	0.000	0.375	Up	0.040	0.084	0.049	0.069
GO:0009059	385	0.192	0.197	Down	0.040	0.084	0.001	0.008
GO:0016570	11	0.273	0.273	Down	0.040	0.084	0.004	0.014
GO:0046486	25	0.160	0.320	Up	0.040	0.085	0.005	0.015
GO:0043038	40	0.350	0.200	Down	0.040	0.085	0.005	0.015
GO:0018344	3	0.000	0.333	Up	0.040	0.085	0.097	0.119
GO:0006091	41	0.317	0.146	Down	0.041	0.085	0.004	0.012
GO:0044265	97	0.299	0.165	Down	0.041	0.085	0.004	0.013
GO:0006166	2	1.000	0.000	Down	0.041	0.085	0.041	0.060
GO:0032787	53	0.264	0.151	Down	0.041	0.085	0.010	0.023
GO:0032269	1	0.000	1.000	Up	0.041	0.086	0.041	0.060
GO:0043039	40	0.350	0.200	Down	0.042	0.086	0.006	0.016
GO:0016569	11	0.273	0.273	Down	0.042	0.086	0.005	0.015
GO:0006415	5	0.000	0.400	Up	0.042	0.086	0.147	0.174
GO:0008652	20	0.150	0.200	Down	0.042	0.086	0.018	0.034
GO:0043101	2	1.000	0.000	Down	0.042	0.086	0.042	0.061
GO:1902578	203	0.153	0.182	Up	0.042	0.086	0.005	0.015
GO:0006084	5	0.000	0.400	Up	0.042	0.087	0.056	0.076
GO:0043174	2	1.000	0.000	Down	0.043	0.087	0.043	0.062
GO:0043624	5	0.000	0.400	Up	0.043	0.087	0.143	0.169
GO:0051248	1	0.000	1.000	Up	0.043	0.088	0.043	0.062
GO:0072524	12	0.417	0.000	Down	0.044	0.088	0.074	0.095
GO:0071103	19	0.316	0.211	Down	0.044	0.088	0.009	0.021
GO:0009057	101	0.287	0.158	Down	0.044	0.088	0.006	0.017
GO:1901135	97	0.175	0.258	Up	0.044	0.088	0.001	0.008
GO:1901070	2	0.000	0.500	Up	0.044	0.088	0.013	0.028
GO:0043650	3	0.333	0.000	Down	0.045	0.089	0.058	0.078
GO:0030154	7	0.000	0.286	Up	0.045	0.090	0.065	0.087
GO:0002376	7	0.286	0.000	Down	0.045	0.090	0.020	0.037
GO:0032984	8	0.000	0.375	Up	0.046	0.091	0.055	0.075
GO:0006473	6	0.000	0.500	Up	0.046	0.091	0.116	0.140
GO:0022411	8	0.000	0.375	Up	0.046	0.092	0.053	0.073
GO:0006412	231	0.229	0.173	Down	0.047	0.093	0.004	0.013
GO:0030163	86	0.302	0.174	Down	0.047	0.093	0.004	0.012
GO:0043484	2	0.500	0.000	Down	0.048	0.094	0.091	0.113
GO:0051130	3	0.333	0.000	Down	0.048	0.094	0.166	0.195
GO:0009991	7	0.429	0.143	Down	0.048	0.094	0.019	0.036
GO:0001522	17	0.059	0.176	Up	0.048	0.094	0.051	0.071
GO:0031365	4	0.250	0.000	Down	0.048	0.094	0.069	0.090
GO:0018345	8	0.000	0.500	Up	0.049	0.095	0.068	0.090
GO:0040011	58	0.155	0.207	Up	0.049	0.095	0.004	0.013
GO:0044765	199	0.156	0.176	Up	0.049	0.095	0.003	0.011
GO:0006400	19	0.105	0.263	Up	0.049	0.095	0.003	0.011
GO:0006420	3	0.000	0.667	Up	0.049	0.095	0.146	0.172
GO:0051252	87	0.195	0.161	Down	0.049	0.095	0.010	0.023
GO:0006749	4	0.250	0.500	Up	0.050	0.096	0.012	0.026
GO:0006260	47	0.106	0.170	Up	0.050	0.096	0.020	0.037
GO:0044248	137	0.255	0.161	Down	0.050	0.096	0.005	0.014
GO:0046165	6	0.167	0.000	Down	0.051	0.097	0.079	0.101
GO:0006793	226	0.159	0.186	Up	0.052	0.099	0.003	0.012
GO:0009218	2	0.000	0.500	Up	0.053	0.102	0.018	0.035
GO:0006275	3	0.000	0.333	Up	0.054	0.102	0.085	0.107
GO:0051649	138	0.188	0.109	Down	0.054	0.102	0.006	0.015
GO:0046131	2	0.000	0.500	Up	0.054	0.102	0.015	0.030
GO:0051028	4	0.250	0.250	Down	0.054	0.102	0.033	0.053
GO:0051641	142	0.183	0.120	Down	0.054	0.102	0.003	0.012
GO:0030433	19	0.158	0.211	Up	0.054	0.102	0.027	0.047
GO:0015748	6	0.167	0.167	Down	0.054	0.102	0.003	0.010
GO:0055086	85	0.235	0.141	Down	0.055	0.102	0.004	0.012
GO:0023051	21	0.238	0.286	Up	0.055	0.102	0.001	0.006
GO:0006383	7	0.286	0.143	Down	0.055	0.103	0.006	0.017
GO:0034982	2	0.500	0.000	Down	0.055	0.103	0.056	0.076
GO:0052126	54	0.167	0.185	Up	0.055	0.103	0.004	0.013
GO:0042273	16	0.250	0.125	Down	0.056	0.104	0.035	0.054
GO:0009966	21	0.238	0.286	Up	0.056	0.104	0.001	0.006
GO:0052192	54	0.167	0.185	Up	0.056	0.104	0.004	0.012
GO:0033013	8	0.000	0.375	Up	0.056	0.104	0.079	0.101
GO:0010646	21	0.238	0.286	Up	0.056	0.104	0.001	0.006
GO:0046134	2	0.000	0.500	Up	0.057	0.105	0.019	0.036
GO:0009220	2	0.000	0.500	Up	0.057	0.105	0.017	0.032
GO:0006367	8	0.000	0.375	Up	0.057	0.105	0.036	0.055
GO:0020027	7	0.143	0.286	Up	0.058	0.106	0.010	0.023
GO:0006388	2	0.000	0.500	Up	0.058	0.106	0.067	0.089
GO:0031325	4	0.500	0.250	Down	0.058	0.106	0.013	0.028
GO:0000394	2	0.000	0.500	Up	0.058	0.106	0.075	0.096
GO:0046132	2	0.000	0.500	Up	0.058	0.106	0.015	0.030
GO:0010604	4	0.500	0.250	Down	0.059	0.106	0.016	0.032
GO:0042168	8	0.000	0.375	Up	0.059	0.106	0.086	0.108
GO:0006656	4	0.250	0.000	Down	0.059	0.106	0.038	0.057
GO:1902589	44	0.182	0.159	Down	0.059	0.106	0.003	0.012
GO:0008104	148	0.189	0.128	Down	0.059	0.106	0.007	0.017
GO:0006213	2	0.000	0.500	Up	0.060	0.107	0.017	0.032
GO:0009127	11	0.091	0.364	Up	0.060	0.107	0.051	0.071
GO:0015980	24	0.125	0.250	Up	0.060	0.107	0.030	0.050
GO:0006650	24	0.167	0.333	Up	0.060	0.107	0.005	0.015
GO:0042594	3	0.667	0.000	Down	0.060	0.107	0.044	0.063
GO:0042440	8	0.000	0.375	Up	0.060	0.107	0.084	0.107
GO:0006811	79	0.177	0.190	Down	0.061	0.108	0.003	0.011
GO:0042439	4	0.250	0.000	Down	0.061	0.108	0.037	0.056
GO:0046470	4	0.250	0.000	Down	0.061	0.108	0.032	0.052
GO:0031668	5	0.400	0.000	Down	0.061	0.108	0.115	0.139
GO:0043094	3	0.667	0.000	Down	0.062	0.109	0.092	0.114
GO:0051806	42	0.167	0.214	Up	0.062	0.109	0.002	0.009
GO:0046395	7	0.143	0.429	Up	0.062	0.109	0.062	0.083
GO:0016054	7	0.143	0.429	Up	0.063	0.110	0.067	0.089
GO:0009168	11	0.091	0.364	Up	0.063	0.110	0.056	0.076
GO:0022402	21	0.095	0.190	Up	0.063	0.110	0.056	0.076
GO:0006778	8	0.000	0.375	Up	0.063	0.110	0.085	0.107
GO:0045333	23	0.130	0.261	Up	0.063	0.110	0.029	0.049
GO:0048869	8	0.000	0.250	Up	0.063	0.110	0.077	0.098
GO:0071702	174	0.178	0.126	Down	0.063	0.110	0.009	0.021
GO:0034033	4	0.000	0.250	Up	0.064	0.110	0.042	0.061
GO:0030260	42	0.167	0.214	Up	0.064	0.110	0.003	0.011
GO:0017038	19	0.263	0.053	Down	0.064	0.110	0.054	0.074
GO:2001141	85	0.188	0.165	Down	0.065	0.110	0.010	0.022
GO:0042540	7	0.143	0.286	Up	0.065	0.110	0.012	0.026
GO:0034030	4	0.000	0.250	Up	0.065	0.110	0.041	0.060
GO:0015936	4	0.000	0.250	Up	0.065	0.110	0.041	0.060
GO:0030488	4	0.000	0.250	Up	0.065	0.110	0.050	0.069
GO:0046907	134	0.179	0.112	Down	0.065	0.110	0.006	0.016
GO:0051179	346	0.171	0.159	Up	0.065	0.110	0.004	0.013
GO:0015711	18	0.167	0.111	Down	0.065	0.110	0.010	0.022
GO:0045184	143	0.189	0.119	Down	0.065	0.110	0.008	0.020
GO:0006418	38	0.342	0.211	Down	0.066	0.111	0.007	0.018
GO:0009893	4	0.500	0.250	Down	0.066	0.111	0.016	0.032
GO:0033866	4	0.000	0.250	Up	0.066	0.111	0.041	0.060
GO:0033875	4	0.000	0.250	Up	0.066	0.111	0.041	0.060
GO:0072528	14	0.286	0.143	Down	0.066	0.111	0.001	0.007
GO:0044282	7	0.143	0.429	Up	0.066	0.111	0.065	0.087
GO:0016311	15	0.200	0.267	Down	0.066	0.111	0.007	0.018
GO:0015031	142	0.190	0.120	Down	0.066	0.111	0.007	0.018
GO:0034032	4	0.000	0.250	Up	0.067	0.112	0.038	0.057
GO:0033865	4	0.000	0.250	Up	0.067	0.112	0.044	0.063
GO:0055085	69	0.174	0.188	Up	0.067	0.112	0.006	0.016
GO:0006355	85	0.188	0.165	Down	0.068	0.113	0.012	0.026
GO:0009148	2	0.000	0.500	Up	0.068	0.113	0.045	0.064
GO:0044409	46	0.174	0.196	Up	0.068	0.113	0.003	0.011
GO:0030522	2	0.500	0.000	Down	0.069	0.114	0.020	0.037
GO:0006733	15	0.333	0.133	Down	0.070	0.115	0.022	0.039
GO:0002682	6	0.333	0.000	Down	0.070	0.115	0.024	0.043
GO:0046916	3	0.333	0.667	Up	0.070	0.115	0.005	0.014
GO:0015937	4	0.000	0.250	Up	0.070	0.115	0.045	0.064
GO:0060627	23	0.087	0.261	Up	0.071	0.115	0.003	0.011
GO:0019637	115	0.217	0.191	Down	0.071	0.115	0.002	0.009
GO:0015693	1	0.000	1.000	Up	0.071	0.116	0.071	0.092
GO:0071496	5	0.400	0.000	Down	0.071	0.116	0.116	0.140
GO:0017004	2	0.500	0.500	Up	0.071	0.116	0.030	0.049
GO:0000393	5	0.400	0.400	Down	0.071	0.116	0.008	0.019
GO:0006887	5	0.400	0.200	Down	0.071	0.116	0.000	0.005
GO:0071822	51	0.235	0.196	Down	0.071	0.116	0.004	0.013
GO:0042180	6	0.000	0.333	Up	0.072	0.116	0.067	0.089
GO:0009150	40	0.150	0.250	Up	0.072	0.116	0.003	0.011
GO:0051828	46	0.174	0.196	Up	0.073	0.117	0.002	0.009
GO:0046903	5	0.400	0.200	Down	0.074	0.119	0.000	0.004
GO:0050776	6	0.333	0.000	Down	0.074	0.119	0.022	0.040
GO:0055076	3	0.333	0.667	Up	0.075	0.120	0.005	0.015
GO:0032940	5	0.400	0.200	Down	0.075	0.120	0.000	0.004
GO:0042181	6	0.000	0.333	Up	0.075	0.120	0.072	0.093
GO:0006886	102	0.196	0.108	Down	0.076	0.121	0.009	0.021
GO:0034613	106	0.189	0.123	Down	0.077	0.122	0.007	0.017
GO:0051234	333	0.171	0.150	Up	0.077	0.122	0.004	0.012
GO:0070727	106	0.189	0.123	Down	0.078	0.123	0.007	0.018
GO:1901661	6	0.000	0.333	Up	0.078	0.124	0.077	0.098
GO:0006796	219	0.164	0.178	Up	0.078	0.124	0.003	0.012
GO:0006810	332	0.172	0.151	Up	0.079	0.125	0.004	0.013
GO:0006487	2	0.000	0.500	Up	0.080	0.126	0.172	0.202
GO:0017183	5	0.200	0.400	Up	0.081	0.127	0.016	0.032
GO:0007017	31	0.194	0.194	Up	0.081	0.127	0.003	0.012
GO:0009124	12	0.083	0.333	Up	0.081	0.127	0.058	0.079
GO:1901663	6	0.000	0.333	Up	0.082	0.128	0.075	0.096
GO:0048870	10	0.100	0.300	Up	0.082	0.128	0.050	0.069
GO:0055114	95	0.211	0.221	Up	0.082	0.128	0.001	0.007
GO:0006873	11	0.091	0.364	Up	0.082	0.128	0.014	0.029
GO:0030003	11	0.091	0.364	Up	0.083	0.129	0.014	0.029
GO:0009156	12	0.083	0.333	Up	0.084	0.131	0.061	0.082
GO:0009259	41	0.146	0.244	Up	0.084	0.131	0.004	0.013
GO:0046034	12	0.167	0.417	Up	0.084	0.131	0.029	0.049
GO:0051674	10	0.100	0.300	Up	0.086	0.132	0.053	0.073
GO:0017182	5	0.200	0.400	Up	0.086	0.132	0.016	0.031
GO:0007186	4	0.000	0.250	Up	0.087	0.135	0.175	0.205
GO:0006366	21	0.143	0.238	Up	0.088	0.135	0.015	0.029
GO:0031667	4	0.500	0.250	Down	0.088	0.136	0.007	0.018
GO:0019693	42	0.143	0.238	Up	0.089	0.136	0.004	0.014
GO:0015988	14	0.214	0.357	Up	0.089	0.136	0.003	0.012
GO:0034227	3	0.000	0.333	Up	0.089	0.137	0.136	0.161
GO:0015991	14	0.214	0.357	Up	0.090	0.138	0.003	0.011
GO:0006826	3	0.333	0.000	Down	0.091	0.138	0.069	0.090
GO:0046488	18	0.167	0.333	Up	0.091	0.138	0.010	0.023
GO:0098655	17	0.176	0.294	Up	0.091	0.139	0.009	0.021
GO:1901657	48	0.208	0.229	Down	0.092	0.139	0.001	0.007
GO:0048878	14	0.143	0.357	Up	0.092	0.140	0.005	0.015
GO:0015684	3	0.333	0.000	Down	0.093	0.140	0.072	0.093
GO:0030150	3	0.667	0.000	Down	0.094	0.142	0.043	0.062
GO:0009199	30	0.167	0.300	Up	0.095	0.144	0.002	0.010
GO:0034220	19	0.211	0.263	Up	0.096	0.144	0.001	0.006
GO:0098660	17	0.176	0.294	Up	0.097	0.146	0.010	0.023
GO:0070271	42	0.262	0.190	Down	0.097	0.146	0.006	0.015
GO:0051259	6	0.167	0.167	Up	0.097	0.146	0.027	0.046
GO:0098662	17	0.176	0.294	Up	0.098	0.146	0.010	0.023
GO:0006461	42	0.262	0.190	Down	0.098	0.146	0.005	0.015
GO:0006817	22	0.136	0.045	Down	0.100	0.149	0.261	0.292
GO:0006334	6	0.333	0.333	Down	0.100	0.149	0.020	0.037
GO:0009205	30	0.167	0.300	Up	0.100	0.149	0.002	0.010
GO:0030258	4	0.250	0.250	Down	0.100	0.149	0.064	0.085
GO:0034728	6	0.333	0.333	Down	0.101	0.149	0.022	0.040
GO:0000278	13	0.000	0.154	Up	0.101	0.149	0.246	0.276
GO:0006665	2	0.000	1.000	Up	0.101	0.150	0.103	0.127
GO:0044283	59	0.119	0.186	Up	0.102	0.151	0.012	0.026
GO:1901615	13	0.154	0.000	Down	0.104	0.153	0.231	0.261
GO:0071705	16	0.188	0.125	Down	0.105	0.154	0.024	0.043
GO:0071824	11	0.273	0.182	Down	0.105	0.154	0.043	0.062
GO:0007166	8	0.125	0.125	Up	0.105	0.154	0.036	0.056
GO:0065004	11	0.273	0.182	Down	0.105	0.154	0.043	0.062
GO:0009116	47	0.213	0.234	Down	0.106	0.154	0.002	0.008
GO:0009117	71	0.211	0.155	Down	0.106	0.154	0.004	0.013
GO:0006825	3	0.000	0.333	Up	0.106	0.154	0.113	0.138
GO:0010256	4	0.000	0.250	Up	0.106	0.154	0.189	0.219
GO:0006310	18	0.167	0.111	Down	0.106	0.154	0.020	0.037
GO:0006220	8	0.250	0.125	Up	0.107	0.155	0.032	0.052
GO:0015074	3	0.333	0.000	Down	0.108	0.156	0.120	0.144
GO:0009165	36	0.194	0.194	Up	0.108	0.156	0.002	0.010
GO:0006376	3	0.333	0.333	Down	0.108	0.156	0.033	0.053
GO:0000003	3	0.333	0.000	Down	0.108	0.156	0.172	0.202
GO:0032483	13	0.231	0.231	Down	0.109	0.157	0.008	0.019
GO:0072527	15	0.267	0.133	Up	0.109	0.157	0.003	0.011
GO:0055082	12	0.083	0.333	Up	0.109	0.157	0.017	0.032
GO:0032313	13	0.231	0.231	Down	0.109	0.157	0.009	0.021
GO:1901293	37	0.189	0.189	Up	0.111	0.158	0.003	0.011
GO:0015698	23	0.130	0.087	Down	0.111	0.159	0.214	0.243
GO:0050801	12	0.167	0.333	Up	0.112	0.160	0.005	0.014
GO:0055080	12	0.167	0.333	Up	0.113	0.160	0.005	0.015
GO:1901565	31	0.161	0.161	Down	0.113	0.161	0.033	0.053
GO:0016192	83	0.145	0.157	Up	0.113	0.161	0.009	0.021
GO:1902600	16	0.188	0.312	Up	0.114	0.161	0.008	0.020
GO:0010498	21	0.190	0.190	Up	0.114	0.162	0.030	0.050
GO:0006766	8	0.125	0.250	Up	0.116	0.164	0.034	0.054
GO:0043161	21	0.190	0.190	Up	0.117	0.165	0.033	0.053
GO:0007154	59	0.169	0.102	Down	0.119	0.168	0.013	0.027
GO:0006352	14	0.071	0.286	Up	0.120	0.168	0.031	0.051
GO:0045047	7	0.143	0.143	Down	0.120	0.168	0.048	0.067
GO:0006163	43	0.163	0.233	Up	0.120	0.168	0.003	0.010
GO:0009144	31	0.194	0.290	Up	0.120	0.169	0.002	0.009
GO:0072599	7	0.143	0.143	Down	0.122	0.171	0.047	0.066
GO:0006612	7	0.143	0.143	Down	0.122	0.171	0.047	0.067
GO:1903047	12	0.000	0.167	Up	0.123	0.171	0.282	0.313
GO:0051260	3	0.333	0.000	Down	0.123	0.172	0.219	0.249
GO:0042364	8	0.125	0.250	Up	0.125	0.174	0.038	0.057
GO:0043623	26	0.308	0.192	Down	0.126	0.175	0.007	0.018
GO:0009262	7	0.143	0.143	Up	0.126	0.175	0.030	0.049
GO:0006767	8	0.125	0.250	Up	0.126	0.175	0.039	0.059
GO:0008295	3	0.000	0.333	Up	0.128	0.177	0.072	0.093
GO:0009110	8	0.125	0.250	Up	0.128	0.178	0.041	0.060
GO:0042401	3	0.000	0.333	Up	0.132	0.182	0.073	0.094
GO:1902582	80	0.162	0.125	Down	0.132	0.182	0.017	0.032
GO:0006753	73	0.205	0.151	Down	0.132	0.182	0.005	0.014
GO:0006596	3	0.000	0.333	Up	0.132	0.182	0.076	0.097
GO:0006261	27	0.148	0.222	Up	0.133	0.182	0.035	0.054
GO:0016567	11	0.182	0.182	Down	0.133	0.182	0.021	0.039
GO:0019751	3	0.333	0.000	Down	0.134	0.183	0.241	0.270
GO:0006744	5	0.000	0.400	Up	0.134	0.184	0.096	0.118
GO:0009309	3	0.000	0.333	Up	0.135	0.184	0.073	0.094
GO:0006743	5	0.000	0.400	Up	0.137	0.187	0.105	0.128
GO:0009119	46	0.196	0.239	Down	0.137	0.187	0.001	0.008
GO:0051258	8	0.000	0.250	Up	0.137	0.187	0.269	0.301
GO:0006536	5	0.200	0.000	Down	0.139	0.188	0.096	0.119
GO:0009141	34	0.176	0.265	Up	0.139	0.188	0.005	0.015
GO:1901617	9	0.111	0.000	Down	0.139	0.189	0.207	0.238
GO:0006772	4	0.250	0.250	Up	0.139	0.189	0.031	0.051
GO:0043413	7	0.000	0.286	Up	0.140	0.189	0.212	0.242
GO:0009228	4	0.250	0.250	Up	0.142	0.192	0.034	0.053
GO:0046128	41	0.171	0.244	Up	0.143	0.192	0.003	0.012
GO:0042278	41	0.171	0.244	Up	0.143	0.192	0.004	0.013
GO:0006323	10	0.200	0.200	Down	0.143	0.192	0.056	0.077
GO:0009263	4	0.000	0.250	Up	0.143	0.192	0.056	0.076
GO:0006486	7	0.000	0.286	Up	0.144	0.192	0.207	0.238
GO:0042724	4	0.250	0.250	Up	0.144	0.192	0.033	0.053
GO:0032392	6	0.333	0.167	Down	0.145	0.193	0.071	0.092
GO:0009101	7	0.000	0.286	Up	0.145	0.193	0.207	0.238
GO:0042723	4	0.250	0.250	Up	0.146	0.194	0.033	0.053
GO:0070085	7	0.000	0.286	Up	0.146	0.194	0.212	0.242
GO:0044262	11	0.273	0.091	Down	0.146	0.194	0.098	0.121
GO:0009100	7	0.000	0.286	Up	0.147	0.195	0.212	0.242
GO:0008643	4	0.000	0.250	Up	0.148	0.195	0.271	0.302
GO:0007165	54	0.148	0.111	Up	0.148	0.196	0.016	0.032
GO:0032508	6	0.333	0.167	Down	0.149	0.196	0.070	0.091
GO:0006470	11	0.182	0.364	Up	0.149	0.196	0.020	0.037
GO:0023052	54	0.148	0.111	Up	0.150	0.197	0.014	0.028
GO:0006401	10	0.200	0.100	Down	0.150	0.197	0.090	0.113
GO:0010639	3	0.333	0.333	Down	0.150	0.197	0.034	0.054
GO:0006432	3	0.333	0.000	Up	0.151	0.197	0.082	0.104
GO:0051494	3	0.333	0.333	Down	0.151	0.197	0.038	0.057
GO:0018202	6	0.167	0.333	Up	0.151	0.197	0.045	0.064
GO:1901658	19	0.158	0.158	Down	0.151	0.198	0.032	0.052
GO:0006631	29	0.103	0.172	Up	0.152	0.198	0.226	0.255
GO:0042454	19	0.158	0.158	Down	0.152	0.198	0.028	0.047
GO:0019439	37	0.162	0.108	Down	0.152	0.198	0.036	0.055
GO:0044700	54	0.148	0.111	Up	0.154	0.200	0.015	0.030
GO:0006152	19	0.158	0.158	Down	0.154	0.200	0.030	0.050
GO:0046130	19	0.158	0.158	Down	0.155	0.201	0.032	0.052
GO:1901361	39	0.154	0.103	Down	0.157	0.203	0.036	0.056
GO:0030837	3	0.333	0.333	Down	0.157	0.203	0.038	0.057
GO:0032446	18	0.167	0.167	Down	0.158	0.203	0.022	0.040
GO:0009207	17	0.176	0.176	Down	0.159	0.204	0.024	0.042
GO:0031333	3	0.333	0.333	Down	0.159	0.204	0.037	0.057
GO:0046700	39	0.154	0.103	Down	0.159	0.204	0.040	0.060
GO:0048193	26	0.115	0.192	Up	0.160	0.204	0.028	0.048
GO:0051129	3	0.333	0.333	Down	0.160	0.204	0.040	0.059
GO:0000956	5	0.200	0.000	Down	0.160	0.204	0.279	0.310
GO:1901069	17	0.176	0.176	Down	0.160	0.204	0.020	0.037
GO:0032272	3	0.333	0.333	Down	0.160	0.204	0.038	0.058
GO:0031497	7	0.286	0.286	Down	0.161	0.205	0.027	0.047
GO:0009146	17	0.176	0.176	Down	0.162	0.206	0.024	0.042
GO:0072523	19	0.158	0.158	Down	0.162	0.206	0.033	0.053
GO:0006195	18	0.167	0.167	Down	0.162	0.206	0.028	0.047
GO:0009164	19	0.158	0.158	Down	0.162	0.206	0.029	0.049
GO:0009261	18	0.167	0.167	Down	0.163	0.206	0.029	0.049
GO:0048522	8	0.250	0.125	Down	0.163	0.206	0.075	0.096
GO:0009154	18	0.167	0.167	Down	0.164	0.207	0.027	0.047
GO:0006184	17	0.176	0.176	Down	0.164	0.207	0.023	0.041
GO:0034655	35	0.171	0.114	Down	0.165	0.208	0.033	0.053
GO:0000041	7	0.143	0.143	Up	0.165	0.208	0.034	0.054
GO:0009203	17	0.176	0.176	Down	0.167	0.210	0.020	0.037
GO:0006544	4	0.000	0.500	Up	0.168	0.210	0.196	0.227
GO:0044270	39	0.154	0.103	Down	0.168	0.210	0.043	0.062
GO:0015992	19	0.211	0.263	Up	0.169	0.211	0.006	0.015
GO:0006446	9	0.222	0.222	Up	0.170	0.212	0.022	0.040
GO:1901136	23	0.174	0.130	Down	0.171	0.213	0.042	0.060
GO:0006818	19	0.211	0.263	Up	0.172	0.215	0.006	0.017
GO:0006284	4	0.500	0.000	Down	0.172	0.215	0.087	0.109
GO:0051052	4	0.000	0.250	Up	0.174	0.216	0.067	0.089
GO:0006298	8	0.000	0.250	Up	0.177	0.220	0.213	0.242
GO:0070838	6	0.333	0.333	Down	0.178	0.220	0.011	0.023
GO:0070972	8	0.125	0.250	Down	0.181	0.224	0.023	0.041
GO:0043604	5	0.000	0.400	Up	0.182	0.225	0.121	0.145
GO:0072511	6	0.333	0.333	Down	0.183	0.226	0.012	0.025
GO:0051169	25	0.160	0.040	Down	0.183	0.226	0.195	0.226
GO:0006118	4	0.000	0.250	Up	0.186	0.229	0.313	0.344
GO:0006913	25	0.160	0.040	Down	0.187	0.230	0.199	0.230
GO:1901068	19	0.158	0.211	Down	0.188	0.231	0.008	0.020
GO:0008216	4	0.250	0.250	Down	0.188	0.231	0.044	0.063
GO:0072521	48	0.188	0.208	Up	0.190	0.233	0.003	0.011
GO:0006434	3	0.333	0.000	Down	0.191	0.234	0.152	0.180
GO:0009186	4	0.250	0.250	Up	0.192	0.235	0.019	0.036
GO:0006595	4	0.250	0.250	Down	0.197	0.240	0.041	0.060
GO:0006221	7	0.286	0.143	Down	0.199	0.243	0.028	0.047
GO:0006402	7	0.143	0.000	Down	0.200	0.244	0.237	0.267
GO:0046039	18	0.167	0.222	Down	0.202	0.246	0.008	0.020
GO:0044417	4	0.000	0.250	Up	0.202	0.246	0.119	0.144
GO:0031334	2	0.000	0.000	Down	0.207	0.252	0.366	0.395
GO:0042274	9	0.222	0.222	Down	0.209	0.253	0.023	0.041
GO:0044053	4	0.000	0.250	Up	0.209	0.253	0.124	0.148
GO:0051836	4	0.000	0.250	Up	0.209	0.253	0.118	0.143
GO:0042000	4	0.000	0.250	Up	0.209	0.253	0.117	0.142
GO:0010638	2	0.000	0.000	Down	0.210	0.253	0.372	0.400
GO:0051808	4	0.000	0.250	Up	0.212	0.254	0.118	0.142
GO:0035556	36	0.167	0.111	Down	0.212	0.254	0.034	0.053
GO:0006855	3	0.000	0.000	Up	0.212	0.254	0.218	0.248
GO:0051495	2	0.000	0.000	Down	0.212	0.254	0.373	0.401
GO:0072330	21	0.095	0.143	Up	0.212	0.254	0.288	0.318
GO:0030838	2	0.000	0.000	Down	0.212	0.254	0.369	0.397
GO:1902579	4	0.000	0.250	Up	0.215	0.256	0.121	0.145
GO:0015931	11	0.182	0.182	Down	0.215	0.256	0.054	0.074
GO:0045010	2	0.000	0.000	Down	0.216	0.258	0.371	0.399
GO:0044766	4	0.000	0.250	Up	0.216	0.258	0.125	0.149
GO:0032273	2	0.000	0.000	Down	0.217	0.259	0.379	0.407
GO:0009166	19	0.158	0.158	Down	0.219	0.260	0.039	0.058
GO:0015893	3	0.000	0.000	Up	0.221	0.262	0.223	0.252
GO:0071897	1	0.000	0.000	Up	0.223	0.264	0.223	0.252
GO:0015858	3	0.000	0.333	Up	0.226	0.267	0.202	0.233
GO:0006633	19	0.105	0.158	Up	0.229	0.271	0.240	0.270
GO:0009143	18	0.167	0.167	Down	0.232	0.275	0.035	0.054
GO:0006333	12	0.250	0.250	Down	0.236	0.279	0.049	0.069
GO:0030261	2	0.000	0.000	Down	0.237	0.279	0.360	0.390
GO:0006914	6	0.333	0.000	Down	0.238	0.280	0.203	0.234
GO:0009126	17	0.118	0.294	Up	0.239	0.281	0.089	0.111
GO:0009167	17	0.118	0.294	Up	0.239	0.281	0.092	0.114
GO:0006405	4	0.250	0.250	Down	0.241	0.283	0.053	0.073
GO:0009064	9	0.111	0.111	Down	0.250	0.293	0.078	0.099
GO:0006512	5	0.400	0.000	Down	0.255	0.298	0.099	0.121
GO:0046434	22	0.182	0.136	Down	0.259	0.303	0.041	0.060
GO:0051247	3	0.333	0.333	Up	0.260	0.303	0.038	0.057
GO:0015849	13	0.154	0.077	Down	0.260	0.303	0.094	0.117
GO:0032270	3	0.333	0.333	Up	0.262	0.305	0.035	0.054
GO:0007034	5	0.200	0.200	Down	0.263	0.306	0.042	0.061
GO:0052652	2	0.500	0.000	Down	0.264	0.306	0.115	0.139
GO:0046068	2	0.500	0.000	Down	0.268	0.311	0.114	0.138
GO:0046394	39	0.128	0.179	Up	0.271	0.314	0.045	0.063
GO:0009063	6	0.167	0.333	Up	0.271	0.314	0.172	0.202
GO:0046942	13	0.154	0.077	Down	0.272	0.314	0.098	0.120
GO:1901264	5	0.000	0.200	Up	0.274	0.316	0.300	0.330
GO:0016053	39	0.128	0.179	Up	0.276	0.318	0.050	0.069
GO:0000226	5	0.000	0.200	Up	0.278	0.320	0.387	0.414
GO:1901606	6	0.167	0.333	Up	0.278	0.320	0.175	0.204
GO:0044093	4	0.250	0.250	Down	0.280	0.322	0.064	0.085
GO:0009123	18	0.111	0.278	Up	0.282	0.323	0.087	0.109
GO:0019692	3	0.333	0.000	Down	0.282	0.323	0.118	0.143
GO:0043952	5	0.200	0.200	Down	0.285	0.326	0.028	0.048
GO:0009200	3	0.333	0.000	Down	0.286	0.327	0.121	0.145
GO:0043085	4	0.250	0.250	Down	0.287	0.327	0.068	0.089
GO:0009394	3	0.333	0.000	Down	0.287	0.327	0.123	0.147
GO:0007264	24	0.167	0.125	Down	0.290	0.330	0.040	0.060
GO:0006370	3	0.000	0.000	Down	0.292	0.332	0.304	0.334
GO:0009069	7	0.000	0.286	Up	0.293	0.333	0.241	0.270
GO:1901292	20	0.150	0.150	Down	0.294	0.334	0.054	0.074
GO:0009161	18	0.111	0.278	Up	0.295	0.334	0.095	0.117
GO:0040029	3	0.333	0.000	Down	0.303	0.343	0.283	0.314
GO:0006429	2	0.500	0.000	Down	0.306	0.346	0.200	0.231
GO:0006360	3	0.333	0.000	Down	0.307	0.347	0.088	0.110
GO:0006720	7	0.143	0.143	Down	0.311	0.351	0.036	0.055
GO:0007067	11	0.000	0.091	Up	0.311	0.351	0.529	0.550
GO:0008299	7	0.143	0.143	Down	0.315	0.354	0.037	0.057
GO:0016458	3	0.333	0.333	Down	0.315	0.355	0.041	0.060
GO:0006040	4	0.250	0.250	Up	0.318	0.358	0.094	0.116
GO:0016925	4	0.250	0.250	Down	0.322	0.362	0.046	0.065
GO:0006269	2	0.000	0.500	Up	0.325	0.364	0.289	0.320
GO:0006072	5	0.400	0.200	Down	0.327	0.366	0.110	0.135
GO:0052646	6	0.333	0.333	Up	0.329	0.368	0.044	0.062
GO:0007169	3	0.000	0.000	Up	0.344	0.384	0.487	0.512
GO:0006302	5	0.000	0.200	Up	0.347	0.388	0.328	0.359
GO:0007167	3	0.000	0.000	Up	0.351	0.391	0.488	0.512
GO:1901071	3	0.333	0.333	Down	0.355	0.395	0.127	0.152
GO:0009190	3	0.333	0.000	Down	0.355	0.395	0.237	0.267
GO:0051168	8	0.125	0.125	Down	0.364	0.404	0.230	0.260
GO:0000027	8	0.125	0.000	Down	0.365	0.405	0.292	0.322
GO:0006119	3	0.333	0.333	Down	0.372	0.412	0.130	0.155
GO:0002377	3	0.000	0.000	Up	0.377	0.417	0.212	0.242
GO:0002440	3	0.000	0.000	Up	0.377	0.417	0.209	0.240
GO:0070925	15	0.133	0.067	Down	0.380	0.419	0.293	0.323
GO:0042773	3	0.333	0.333	Down	0.381	0.420	0.128	0.152
GO:0009070	2	0.000	0.500	Up	0.382	0.421	0.222	0.252
GO:0009187	4	0.250	0.000	Down	0.390	0.429	0.380	0.408
GO:0008645	2	0.000	0.000	Up	0.391	0.430	0.505	0.530
GO:0015749	2	0.000	0.000	Up	0.394	0.432	0.513	0.537
GO:0006268	2	0.500	0.000	Down	0.395	0.433	0.339	0.368
GO:0006270	11	0.091	0.182	Up	0.396	0.434	0.186	0.216
GO:0009066	4	0.250	0.000	Down	0.397	0.435	0.664	0.676
GO:0009084	3	0.000	0.000	Down	0.399	0.436	0.527	0.549
GO:0006611	3	0.000	0.333	Up	0.412	0.450	0.183	0.213
GO:0006122	2	0.000	0.500	Up	0.413	0.451	0.352	0.381
GO:0042775	2	0.000	0.500	Up	0.417	0.454	0.351	0.381
GO:0006614	5	0.200	0.200	Down	0.433	0.471	0.093	0.115
GO:0006613	5	0.200	0.200	Down	0.436	0.474	0.095	0.117
GO:0030048	4	0.250	0.250	Up	0.437	0.474	0.086	0.108
GO:0050793	4	0.000	0.250	Up	0.438	0.475	0.279	0.310
GO:0046777	1	0.000	0.000	Up	0.440	0.476	0.440	0.465
GO:0000302	3	0.000	0.000	Up	0.440	0.476	0.527	0.549
GO:1901700	3	0.000	0.000	Up	0.441	0.477	0.528	0.549
GO:0006546	3	0.000	0.333	Up	0.444	0.479	0.392	0.419
GO:0010035	3	0.000	0.000	Up	0.445	0.479	0.526	0.549
GO:0009234	2	0.000	0.000	Up	0.445	0.479	0.421	0.447
GO:0007033	4	0.250	0.000	Down	0.445	0.479	0.127	0.151
GO:0006541	2	0.000	0.000	Down	0.446	0.479	0.422	0.447
GO:0009233	2	0.000	0.000	Up	0.449	0.482	0.428	0.453
GO:0006888	20	0.150	0.150	Down	0.450	0.482	0.074	0.095
GO:0009071	3	0.000	0.333	Up	0.453	0.485	0.395	0.421
GO:0006424	3	0.000	0.000	Up	0.459	0.491	0.271	0.302
GO:0009219	2	0.000	0.000	Up	0.462	0.494	0.464	0.490
GO:0006787	2	0.000	0.000	Down	0.467	0.498	0.506	0.530
GO:0097428	1	0.000	0.000	Down	0.469	0.500	0.469	0.494
GO:0048856	4	0.000	0.250	Up	0.476	0.507	0.366	0.395
GO:0006885	8	0.125	0.125	Down	0.477	0.508	0.156	0.184
GO:0033015	2	0.000	0.000	Down	0.478	0.508	0.516	0.539
GO:0055067	8	0.125	0.125	Down	0.489	0.519	0.158	0.186
GO:0016197	3	0.000	0.000	Down	0.497	0.527	0.403	0.428
GO:0006891	3	0.000	0.000	Up	0.498	0.527	0.396	0.422
GO:0042147	3	0.000	0.000	Down	0.504	0.534	0.401	0.427
GO:0000280	14	0.071	0.071	Up	0.505	0.534	0.336	0.366
GO:0048285	14	0.071	0.071	Up	0.514	0.543	0.341	0.370
GO:0015908	3	0.333	0.000	Up	0.519	0.548	0.269	0.301
GO:0000290	3	0.000	0.000	Down	0.534	0.563	0.644	0.661
GO:0000288	3	0.000	0.000	Down	0.535	0.563	0.648	0.663
GO:0006308	4	0.250	0.000	Up	0.551	0.579	0.177	0.206
GO:0000724	2	0.000	0.000	Down	0.565	0.593	0.540	0.559
GO:0000725	2	0.000	0.000	Down	0.571	0.599	0.543	0.561
GO:0042255	11	0.091	0.091	Down	0.580	0.608	0.327	0.358
GO:0008283	3	0.000	0.000	Up	0.581	0.609	0.472	0.497
GO:0000070	2	0.000	0.000	Down	0.599	0.626	0.790	0.799
GO:0000387	4	0.250	0.000	Down	0.600	0.627	0.600	0.618
GO:0000819	2	0.000	0.000	Down	0.618	0.644	0.804	0.811
GO:0022603	2	0.000	0.000	Up	0.619	0.645	0.395	0.421
GO:0051452	7	0.000	0.143	Up	0.645	0.671	0.324	0.356
GO:0045851	7	0.000	0.143	Up	0.647	0.672	0.325	0.356
GO:0030641	7	0.000	0.143	Up	0.650	0.675	0.332	0.362
GO:0030004	7	0.000	0.143	Up	0.650	0.675	0.330	0.361
GO:0051453	7	0.000	0.143	Up	0.653	0.677	0.336	0.366
GO:0007035	7	0.000	0.143	Up	0.655	0.679	0.327	0.358
GO:0022900	7	0.143	0.143	Up	0.680	0.703	0.388	0.415
GO:0022904	6	0.167	0.167	Up	0.682	0.704	0.279	0.310
GO:0006865	4	0.000	0.000	Up	0.682	0.704	0.648	0.663
GO:0009225	4	0.000	0.000	Up	0.693	0.714	0.449	0.474
GO:0034637	3	0.000	0.000	Down	0.705	0.724	0.605	0.622
GO:0019673	3	0.000	0.000	Down	0.705	0.724	0.606	0.622
GO:0016114	2	0.000	0.000	Down	0.706	0.724	0.645	0.662
GO:0000304	2	0.000	0.000	Up	0.706	0.724	0.651	0.665
GO:0009072	3	0.000	0.000	Up	0.707	0.724	0.802	0.810
GO:0009073	3	0.000	0.000	Up	0.707	0.724	0.803	0.811
GO:0006721	2	0.000	0.000	Down	0.713	0.729	0.649	0.663
GO:0006836	1	0.000	0.000	Down	0.718	0.734	0.662	0.676
GO:0051187	3	0.000	0.000	Down	0.737	0.753	0.478	0.503
GO:0051170	10	0.100	0.000	Down	0.745	0.760	0.542	0.561
GO:0044744	10	0.100	0.000	Down	0.747	0.760	0.537	0.557
GO:0034504	10	0.100	0.000	Down	0.747	0.760	0.543	0.561
GO:1902593	10	0.100	0.000	Down	0.748	0.760	0.538	0.557
GO:0006606	10	0.100	0.000	Down	0.749	0.761	0.545	0.562
GO:0000096	3	0.000	0.000	Down	0.768	0.779	0.529	0.550
GO:0060249	3	0.000	0.000	Down	0.791	0.802	0.830	0.836
GO:0000723	3	0.000	0.000	Down	0.799	0.808	0.833	0.837
GO:0032200	3	0.000	0.000	Down	0.800	0.808	0.833	0.837
GO:0006471	3	0.000	0.000	Up	0.800	0.808	0.834	0.837
GO:0031109	3	0.000	0.000	Up	0.803	0.809	0.711	0.721
GO:0007020	3	0.000	0.000	Up	0.803	0.809	0.714	0.723
GO:0046785	3	0.000	0.000	Up	0.807	0.813	0.715	0.723
GO:0009067	3	0.000	0.000	Down	0.864	0.869	0.918	0.918
GO:0042819	3	0.000	0.000	Up	0.877	0.881	0.696	0.708
GO:0042816	3	0.000	0.000	Up	0.882	0.886	0.695	0.708
GO:0008614	3	0.000	0.000	Up	0.883	0.886	0.698	0.709
GO:0009432	2	0.000	0.000	Down	0.921	0.922	0.852	0.853
GO:0072525	4	0.000	0.000	Down	0.921	0.922	0.834	0.837
GO:0006607	3	0.000	0.000	Down	0.926	0.926	0.840	0.842

Also test using limma’s camera

kable(go_cam, digits = 3)

	NGenes	Correlation	Direction	PValue	FDR
GO:0022610	113	0.087	Down	0.002	0.130
GO:0020035	93	0.119	Down	0.002	0.130
GO:0044406	93	0.119	Down	0.002	0.130
GO:0009607	94	0.124	Down	0.003	0.130
GO:0034118	87	0.131	Down	0.003	0.130
GO:0020013	87	0.131	Down	0.003	0.130
GO:0030155	87	0.131	Down	0.003	0.130
GO:0034110	87	0.131	Down	0.003	0.130
GO:0022407	87	0.131	Down	0.003	0.130
GO:0051807	93	0.126	Down	0.003	0.130
GO:0051834	93	0.126	Down	0.003	0.130
GO:0051832	93	0.126	Down	0.003	0.130
GO:0043207	93	0.126	Down	0.003	0.130
GO:0051707	93	0.126	Down	0.003	0.130
GO:0052173	93	0.126	Down	0.003	0.130
GO:0052564	93	0.126	Down	0.003	0.130
GO:0051805	93	0.126	Down	0.003	0.130
GO:0051809	92	0.127	Down	0.003	0.130
GO:0020033	92	0.127	Down	0.003	0.130
GO:0044068	88	0.130	Down	0.003	0.130
GO:0009605	100	0.116	Down	0.003	0.130
GO:0044003	89	0.127	Down	0.003	0.130
GO:0051817	89	0.127	Down	0.003	0.130
GO:0035821	90	0.126	Down	0.004	0.143
GO:0007155	69	0.181	Down	0.004	0.148
GO:0016337	54	0.291	Down	0.005	0.185
GO:0098602	54	0.291	Down	0.005	0.185
GO:0065008	149	0.051	Down	0.007	0.254
GO:0051704	189	0.053	Down	0.008	0.260
GO:0044403	157	0.053	Down	0.009	0.265
GO:0044419	157	0.053	Down	0.009	0.265
GO:0009405	84	0.205	Down	0.010	0.290
GO:0051701	147	0.054	Down	0.010	0.294
GO:0009396	4	-0.061	Down	0.013	0.360
GO:0050896	291	0.030	Down	0.016	0.449
GO:0016485	10	0.039	Down	0.020	0.544
GO:0051604	12	0.024	Down	0.025	0.646
GO:0050789	380	0.018	Down	0.025	0.646
GO:0050794	359	0.017	Down	0.030	0.728
GO:0031123	8	0.032	Up	0.030	0.728
GO:0042026	3	0.098	Down	0.035	0.824
GO:0006206	6	-0.043	Down	0.036	0.824
GO:0008154	1	NA	Down	0.044	0.907
GO:0065007	401	0.019	Down	0.045	0.907
GO:0001817	3	0.171	Down	0.048	0.907
GO:0051239	3	0.171	Down	0.048	0.907
GO:0031167	2	0.374	Down	0.052	0.907
GO:0016255	4	0.220	Up	0.053	0.907
GO:0006094	5	0.365	Down	0.061	0.907
GO:0019319	6	0.310	Down	0.062	0.907
GO:0046364	6	0.310	Down	0.062	0.907
GO:0000245	9	0.064	Down	0.063	0.907
GO:0002098	4	0.005	Up	0.064	0.907
GO:0002097	4	0.005	Up	0.064	0.907
GO:0031399	5	0.019	Up	0.064	0.907
GO:0001932	5	0.019	Up	0.064	0.907
GO:0042325	5	0.019	Up	0.064	0.907
GO:0019856	5	-0.092	Down	0.065	0.907
GO:0006207	5	-0.092	Down	0.065	0.907
GO:0046112	5	-0.092	Down	0.065	0.907
GO:0051051	3	0.257	Up	0.067	0.907
GO:0022616	5	0.065	Up	0.069	0.907
GO:0006271	5	0.065	Up	0.069	0.907
GO:0016571	5	0.090	Down	0.071	0.907
GO:0090151	3	-0.153	Down	0.077	0.907
GO:0007007	3	-0.153	Down	0.077	0.907
GO:0045039	3	-0.153	Down	0.077	0.907
GO:0007006	3	-0.153	Down	0.077	0.907
GO:0006457	72	0.076	Down	0.077	0.907
GO:0006813	4	-0.030	Up	0.078	0.907
GO:0006760	5	-0.033	Down	0.079	0.907
GO:0032507	2	0.148	Up	0.080	0.907
GO:0051651	2	0.148	Up	0.080	0.907
GO:0009112	7	-0.036	Down	0.082	0.907
GO:0032312	2	0.491	Up	0.083	0.907
GO:0006465	7	0.040	Down	0.086	0.907
GO:0006096	17	0.244	Down	0.086	0.907
GO:0018394	4	0.031	Up	0.088	0.907
GO:0006475	4	0.031	Up	0.088	0.907
GO:0018393	4	0.031	Up	0.088	0.907
GO:0016573	4	0.031	Up	0.088	0.907
GO:0006848	2	-0.122	Down	0.088	0.907
GO:0000910	4	0.100	Up	0.092	0.907
GO:0032501	8	0.040	Up	0.099	0.907
GO:0044724	24	0.192	Down	0.100	0.907
GO:0016052	24	0.192	Down	0.100	0.907
GO:0071900	3	0.333	Up	0.100	0.907
GO:0000079	3	0.333	Up	0.100	0.907
GO:0043241	6	-0.014	Up	0.102	0.907
GO:0006338	4	0.002	Down	0.103	0.907
GO:0043603	15	-0.020	Down	0.105	0.907
GO:0009247	12	0.076	Up	0.106	0.907
GO:0046148	6	0.083	Up	0.109	0.907
GO:0033014	6	0.083	Up	0.109	0.907
GO:0006783	6	0.083	Up	0.109	0.907
GO:0006779	6	0.083	Up	0.109	0.907
GO:0046467	13	0.098	Up	0.111	0.907
GO:0007275	6	0.258	Up	0.111	0.907
GO:0035383	7	0.140	Up	0.112	0.907
GO:0006637	7	0.140	Up	0.112	0.907
GO:1901607	11	0.021	Down	0.113	0.907
GO:0044707	7	0.145	Up	0.114	0.907
GO:0016051	12	0.166	Down	0.114	0.907
GO:0006497	18	0.106	Up	0.115	0.907
GO:0042158	18	0.106	Up	0.115	0.907
GO:0042157	18	0.106	Up	0.115	0.907
GO:0006006	12	0.196	Down	0.116	0.907
GO:0006643	15	0.102	Up	0.117	0.907
GO:0006664	13	0.070	Up	0.119	0.907
GO:0009206	8	0.117	Up	0.119	0.907
GO:0009201	8	0.117	Up	0.119	0.907
GO:0043543	15	0.052	Up	0.121	0.907
GO:0043631	6	0.027	Up	0.122	0.907
GO:0009152	17	0.035	Up	0.123	0.907
GO:0042176	3	0.664	Down	0.123	0.907
GO:0034968	4	0.016	Down	0.123	0.907
GO:0006066	7	0.019	Down	0.124	0.907
GO:0019318	14	0.184	Down	0.128	0.907
GO:0005996	14	0.184	Down	0.128	0.907
GO:0097354	6	0.029	Up	0.129	0.907
GO:0018342	6	0.029	Up	0.129	0.907
GO:0043648	10	-0.011	Down	0.132	0.907
GO:0051276	43	0.049	Down	0.132	0.907
GO:0006410	5	-0.053	Up	0.132	0.907
GO:0006506	9	0.201	Up	0.133	0.907
GO:0045859	4	0.091	Up	0.134	0.907
GO:0051338	4	0.091	Up	0.134	0.907
GO:0043549	4	0.091	Up	0.134	0.907
GO:0032784	3	0.212	Down	0.135	0.907
GO:0006518	11	0.002	Down	0.136	0.907
GO:0044767	11	0.138	Up	0.136	0.907
GO:0031338	14	0.037	Up	0.139	0.907
GO:0006730	4	0.007	Down	0.141	0.907
GO:0000154	5	0.080	Down	0.141	0.907
GO:0007005	14	0.031	Down	0.141	0.907
GO:0072655	14	0.031	Down	0.141	0.907
GO:0070585	14	0.031	Down	0.141	0.907
GO:0006626	14	0.031	Down	0.141	0.907
GO:0071616	4	0.230	Up	0.143	0.907
GO:0006085	4	0.230	Up	0.143	0.907
GO:0006086	4	0.230	Up	0.143	0.907
GO:0035384	4	0.230	Up	0.143	0.907
GO:0051188	30	0.051	Up	0.146	0.907
GO:0071976	4	-0.116	Up	0.148	0.907
GO:0006505	10	0.178	Up	0.151	0.907
GO:0009260	18	0.030	Up	0.155	0.907
GO:0070682	6	0.571	Down	0.157	0.907
GO:0006661	10	0.165	Up	0.157	0.907
GO:0032502	12	0.100	Up	0.157	0.907
GO:1902580	33	0.013	Down	0.160	0.907
GO:2000113	4	0.058	Down	0.160	0.907
GO:0010558	4	0.058	Down	0.160	0.907
GO:0045892	4	0.058	Down	0.160	0.907
GO:1902679	4	0.058	Down	0.160	0.907
GO:0051253	4	0.058	Down	0.160	0.907
GO:0051172	4	0.058	Down	0.160	0.907
GO:0045934	4	0.058	Down	0.160	0.907
GO:0044743	6	0.093	Down	0.160	0.907
GO:0051130	3	-0.072	Down	0.162	0.907
GO:0009147	3	0.062	Up	0.162	0.907
GO:0070646	11	-0.028	Down	0.163	0.907
GO:0016579	11	-0.028	Down	0.163	0.907
GO:0046390	19	0.028	Up	0.164	0.907
GO:0008535	1	NA	Up	0.166	0.907
GO:0044272	14	0.044	Up	0.166	0.907
GO:0035890	12	0.016	Up	0.168	0.907
GO:0071826	31	0.050	Down	0.170	0.907
GO:0018344	3	0.027	Up	0.170	0.907
GO:0009890	5	0.108	Down	0.171	0.907
GO:0031327	5	0.108	Down	0.171	0.907
GO:0006473	6	0.100	Up	0.178	0.907
GO:0006817	22	0.005	Down	0.179	0.907
GO:0006084	5	0.297	Up	0.179	0.907
GO:0006378	5	0.013	Up	0.180	0.907
GO:0031124	5	0.013	Up	0.180	0.907
GO:0071840	251	0.024	Down	0.180	0.907
GO:0009628	22	0.051	Down	0.181	0.907
GO:0043624	5	-0.028	Up	0.186	0.907
GO:0006415	5	-0.028	Up	0.186	0.907
GO:0072594	32	0.016	Down	0.186	0.907
GO:0007015	4	0.045	Down	0.187	0.907
GO:0006166	2	0.502	Down	0.188	0.907
GO:0043101	2	0.502	Down	0.188	0.907
GO:0043174	2	0.502	Down	0.188	0.907
GO:0090150	11	0.019	Down	0.188	0.907
GO:0072657	11	0.019	Down	0.188	0.907
GO:0045017	17	0.061	Up	0.189	0.907
GO:0010608	25	0.048	Down	0.190	0.907
GO:0044723	42	0.139	Down	0.190	0.907
GO:0030154	7	0.165	Up	0.191	0.907
GO:0006754	7	0.084	Up	0.192	0.907
GO:0015985	7	0.084	Up	0.192	0.907
GO:0015986	7	0.084	Up	0.192	0.907
GO:0006379	4	0.086	Up	0.192	0.907
GO:0007049	36	0.021	Up	0.193	0.907
GO:0043484	2	-0.051	Down	0.195	0.907
GO:0030029	10	-0.036	Down	0.196	0.907
GO:0006790	20	0.031	Up	0.197	0.907
GO:0065002	11	0.031	Down	0.199	0.907
GO:0006605	34	0.017	Down	0.199	0.907
GO:0042777	1	NA	Up	0.199	0.907
GO:0071806	16	-0.005	Down	0.203	0.907
GO:0018345	8	0.108	Up	0.203	0.907
GO:0048518	11	0.080	Down	0.204	0.907
GO:0043650	3	-0.084	Down	0.205	0.907
GO:0044712	59	0.070	Down	0.205	0.907
GO:0035891	11	0.010	Up	0.208	0.907
GO:0006098	9	0.150	Down	0.209	0.907
GO:0046365	9	0.150	Down	0.209	0.907
GO:0006740	9	0.150	Down	0.209	0.907
GO:0006007	9	0.150	Down	0.209	0.907
GO:0006739	9	0.150	Down	0.209	0.907
GO:0019320	9	0.150	Down	0.209	0.907
GO:0006325	29	0.035	Down	0.210	0.907
GO:0006275	3	-0.107	Up	0.210	0.907
GO:0019362	10	0.132	Down	0.211	0.907
GO:0046496	10	0.132	Down	0.211	0.907
GO:0006081	6	-0.065	Up	0.212	0.907
GO:0006890	6	0.196	Up	0.216	0.907
GO:0006420	3	-0.196	Up	0.216	0.907
GO:0046474	16	0.060	Up	0.216	0.907
GO:0046165	6	0.032	Down	0.216	0.907
GO:0022618	29	0.057	Down	0.217	0.907
GO:0042594	3	0.308	Down	0.218	0.907
GO:0032269	1	NA	Up	0.218	0.907
GO:0051248	1	NA	Up	0.218	0.907
GO:0000394	2	0.143	Up	0.221	0.907
GO:0006388	2	0.143	Up	0.221	0.907
GO:0016568	18	0.016	Down	0.221	0.907
GO:0051235	3	0.041	Up	0.224	0.907
GO:0045185	3	0.041	Up	0.224	0.907
GO:0043094	3	0.233	Down	0.225	0.907
GO:0006487	2	-0.205	Up	0.226	0.907
GO:0071496	5	0.043	Down	0.228	0.907
GO:0031668	5	0.043	Down	0.228	0.907
GO:0043933	107	0.033	Down	0.228	0.907
GO:0006164	19	0.043	Up	0.228	0.907
GO:0005975	53	0.109	Down	0.229	0.907
GO:0044085	153	0.032	Down	0.229	0.907
GO:0015698	23	0.000	Down	0.229	0.907
GO:0006839	18	0.037	Down	0.231	0.907
GO:0008033	37	0.035	Up	0.232	0.907
GO:0034227	3	-0.045	Up	0.234	0.907
GO:0033013	8	0.053	Up	0.235	0.907
GO:0042440	8	0.053	Up	0.235	0.907
GO:0042168	8	0.053	Up	0.235	0.907
GO:0006778	8	0.053	Up	0.235	0.907
GO:0008616	4	-0.058	Down	0.238	0.907
GO:0046116	4	-0.058	Down	0.238	0.907
GO:0009266	21	0.061	Down	0.241	0.907
GO:0034982	2	0.558	Down	0.242	0.907
GO:0008380	81	0.072	Down	0.242	0.907
GO:0022613	98	0.063	Down	0.242	0.907
GO:0010629	6	0.071	Down	0.243	0.907
GO:0007186	4	-0.046	Up	0.245	0.907
GO:0051301	23	0.063	Up	0.246	0.907
GO:0072524	12	0.068	Down	0.246	0.907
GO:0007059	8	0.098	Up	0.246	0.907
GO:0010256	4	0.052	Up	0.246	0.907
GO:0009060	17	0.093	Up	0.248	0.907
GO:0006099	17	0.093	Up	0.248	0.907
GO:0010564	17	0.015	Up	0.248	0.907
GO:0015693	1	NA	Up	0.252	0.907
GO:0009108	24	0.043	Up	0.253	0.907
GO:0043248	8	0.181	Down	0.253	0.907
GO:0009145	9	0.106	Up	0.255	0.907
GO:0000375	64	0.094	Down	0.256	0.907
GO:1901615	13	0.022	Down	0.257	0.907
GO:0033365	33	0.014	Down	0.257	0.907
GO:0009148	2	0.244	Up	0.258	0.907
GO:0050658	7	-0.027	Down	0.259	0.907
GO:0051236	7	-0.027	Down	0.259	0.907
GO:0006403	7	-0.027	Down	0.259	0.907
GO:0050657	7	-0.027	Down	0.259	0.907
GO:0000278	13	0.089	Up	0.263	0.907
GO:0016043	183	0.026	Down	0.264	0.907
GO:0009452	6	0.107	Down	0.264	0.907
GO:0036260	6	0.107	Down	0.264	0.907
GO:0006417	22	0.051	Down	0.265	0.907
GO:0006820	41	0.007	Down	0.265	0.907
GO:0000003	3	0.081	Down	0.270	0.907
GO:0048869	8	0.143	Up	0.270	0.907
GO:0042493	51	0.049	Down	0.271	0.907
GO:0031365	4	0.016	Down	0.274	0.907
GO:0006414	20	0.086	Down	0.282	0.907
GO:0033043	19	0.019	Up	0.284	0.907
GO:0034622	64	0.044	Down	0.284	0.907
GO:0015074	3	0.206	Down	0.285	0.907
GO:0051258	8	0.081	Up	0.286	0.907
GO:0000377	59	0.087	Down	0.287	0.907
GO:0000398	59	0.087	Down	0.287	0.907
GO:1903047	12	0.079	Up	0.287	0.907
GO:0009408	20	0.059	Down	0.288	0.907
GO:0006665	2	0.518	Up	0.289	0.907
GO:1901137	55	0.043	Up	0.290	0.907
GO:0006090	24	0.106	Down	0.290	0.907
GO:0006875	4	0.294	Up	0.293	0.907
GO:0055065	4	0.294	Up	0.293	0.907
GO:0006996	110	0.025	Down	0.293	0.907
GO:0044087	5	-0.161	Down	0.296	0.907
GO:0030833	5	-0.161	Down	0.296	0.907
GO:0032535	5	-0.161	Down	0.296	0.907
GO:0043254	5	-0.161	Down	0.296	0.907
GO:0090066	5	-0.161	Down	0.296	0.907
GO:0032271	5	-0.161	Down	0.296	0.907
GO:0032970	5	-0.161	Down	0.296	0.907
GO:0008064	5	-0.161	Down	0.296	0.907
GO:0032956	5	-0.161	Down	0.296	0.907
GO:0051493	5	-0.161	Down	0.296	0.907
GO:0030832	5	-0.161	Down	0.296	0.907
GO:0042439	4	0.067	Down	0.299	0.907
GO:0046470	4	0.067	Down	0.299	0.907
GO:0006656	4	0.067	Down	0.299	0.907
GO:0042221	68	0.038	Down	0.299	0.907
GO:0051260	3	-0.165	Down	0.301	0.907
GO:0006986	12	0.040	Down	0.301	0.907
GO:0035966	12	0.040	Down	0.301	0.907
GO:0008643	4	0.227	Up	0.302	0.907
GO:0009142	10	0.118	Up	0.303	0.907
GO:0046129	17	0.070	Up	0.305	0.907
GO:0042451	17	0.070	Up	0.305	0.907
GO:0019751	3	0.176	Down	0.307	0.907
GO:0015914	4	0.039	Down	0.314	0.907
GO:0006281	50	0.010	Up	0.316	0.907
GO:0015980	24	0.079	Up	0.316	0.907
GO:0010033	13	0.029	Down	0.318	0.907
GO:0030036	8	-0.074	Down	0.322	0.907
GO:0009127	11	0.065	Up	0.322	0.907
GO:0009168	11	0.065	Up	0.322	0.907
GO:0015937	4	0.243	Up	0.323	0.907
GO:0033866	4	0.243	Up	0.323	0.907
GO:0034032	4	0.243	Up	0.323	0.907
GO:0034033	4	0.243	Up	0.323	0.907
GO:0033875	4	0.243	Up	0.323	0.907
GO:0015936	4	0.243	Up	0.323	0.907
GO:0033865	4	0.243	Up	0.323	0.907
GO:0034030	4	0.243	Up	0.323	0.907
GO:0009132	5	0.120	Up	0.326	0.907
GO:0006357	10	-0.030	Down	0.326	0.907
GO:0000350	3	-0.022	Down	0.327	0.907
GO:0006750	3	-0.117	Up	0.329	0.907
GO:0019184	3	-0.117	Up	0.329	0.907
GO:0043043	3	-0.117	Up	0.329	0.907
GO:0046395	7	-0.029	Up	0.330	0.907
GO:0044282	7	-0.029	Up	0.330	0.907
GO:0016054	7	-0.029	Up	0.330	0.907
GO:0048523	10	-0.001	Down	0.331	0.907
GO:0045333	23	0.078	Up	0.331	0.907
GO:0042181	6	0.158	Up	0.332	0.907
GO:1901661	6	0.158	Up	0.332	0.907
GO:0042180	6	0.158	Up	0.332	0.907
GO:1901663	6	0.158	Up	0.332	0.907
GO:0022402	21	0.031	Up	0.332	0.907
GO:0001522	17	0.018	Up	0.342	0.921
GO:0044106	8	-0.018	Down	0.342	0.921
GO:0009308	8	-0.018	Down	0.342	0.921
GO:0006576	8	-0.018	Down	0.342	0.921
GO:0065003	74	0.039	Down	0.344	0.921
GO:0009066	4	-0.132	Down	0.344	0.921
GO:0032012	3	0.006	Up	0.345	0.921
GO:0042273	16	0.061	Down	0.345	0.921
GO:0042398	11	0.008	Down	0.351	0.921
GO:0000956	5	0.153	Down	0.352	0.921
GO:0042559	6	0.011	Down	0.356	0.921
GO:1901605	24	0.022	Down	0.356	0.921
GO:0010638	2	-0.137	Down	0.356	0.921
GO:0031334	2	-0.137	Down	0.356	0.921
GO:0051495	2	-0.137	Down	0.356	0.921
GO:0030838	2	-0.137	Down	0.356	0.921
GO:0032273	2	-0.137	Down	0.356	0.921
GO:0045010	2	-0.137	Down	0.356	0.921
GO:0032984	8	-0.007	Up	0.356	0.921
GO:0022411	8	-0.007	Up	0.356	0.921
GO:0008213	8	-0.009	Down	0.361	0.928
GO:0006479	8	-0.009	Down	0.361	0.928
GO:0009056	171	0.071	Down	0.362	0.928
GO:0010468	116	0.014	Down	0.365	0.933
GO:0006575	13	0.020	Down	0.369	0.933
GO:0006118	4	0.091	Up	0.369	0.933
GO:0006974	51	0.010	Up	0.371	0.933
GO:0006260	47	0.038	Up	0.372	0.933
GO:0006979	10	0.005	Down	0.373	0.933
GO:1901575	165	0.076	Down	0.374	0.933
GO:0009991	7	0.043	Down	0.374	0.933
GO:0006631	29	0.019	Up	0.375	0.933
GO:0042254	80	0.075	Down	0.375	0.933
GO:0006367	8	0.107	Up	0.379	0.933
GO:1901617	9	0.024	Down	0.380	0.933
GO:0030488	4	0.089	Up	0.382	0.933
GO:0031324	6	0.066	Down	0.384	0.933
GO:0051246	31	0.063	Down	0.385	0.933
GO:0000413	10	0.138	Down	0.388	0.933
GO:0018208	10	0.138	Down	0.388	0.933
GO:0006825	3	0.018	Up	0.389	0.933
GO:0019220	27	0.032	Up	0.391	0.933
GO:0051174	27	0.032	Up	0.391	0.933
GO:0030001	16	0.039	Up	0.392	0.933
GO:0022607	83	0.034	Down	0.394	0.933
GO:0006544	4	0.044	Up	0.394	0.933
GO:0070085	7	0.109	Up	0.394	0.933
GO:0006486	7	0.109	Up	0.394	0.933
GO:0009100	7	0.109	Up	0.394	0.933
GO:0009101	7	0.109	Up	0.394	0.933
GO:0043413	7	0.109	Up	0.394	0.933
GO:0006265	3	-0.090	Down	0.394	0.933
GO:0016482	66	0.045	Down	0.395	0.933
GO:0009124	12	0.048	Up	0.396	0.933
GO:0009156	12	0.048	Up	0.396	0.933
GO:0008610	53	0.039	Up	0.397	0.933
GO:0006364	48	0.050	Down	0.399	0.933
GO:0016072	48	0.050	Down	0.399	0.933
GO:0006511	71	0.100	Down	0.400	0.933
GO:0051128	22	0.017	Up	0.405	0.933
GO:0030433	19	0.028	Up	0.408	0.933
GO:0070647	29	0.040	Down	0.409	0.933
GO:0009892	8	0.052	Down	0.409	0.933
GO:0051186	45	0.040	Up	0.409	0.933
GO:0002376	7	0.046	Down	0.409	0.933
GO:1901264	5	0.250	Up	0.410	0.933
GO:0060255	128	0.017	Down	0.411	0.933
GO:0015858	3	0.390	Up	0.412	0.933
GO:0006520	75	0.034	Down	0.413	0.933
GO:0002682	6	0.158	Down	0.414	0.933
GO:0050776	6	0.158	Down	0.414	0.933
GO:0043086	3	0.068	Down	0.415	0.933
GO:0044092	3	0.068	Down	0.415	0.933
GO:0019752	129	0.031	Down	0.416	0.933
GO:1901070	2	0.028	Up	0.417	0.933
GO:0006897	7	0.015	Down	0.421	0.933
GO:0030261	2	0.127	Down	0.425	0.933
GO:0000226	5	0.096	Up	0.425	0.933
GO:0009438	2	-0.018	Up	0.426	0.933
GO:0046131	2	0.111	Up	0.429	0.933
GO:0009218	2	0.111	Up	0.429	0.933
GO:0009220	2	0.111	Up	0.429	0.933
GO:0046132	2	0.111	Up	0.429	0.933
GO:0046134	2	0.111	Up	0.429	0.933
GO:0006213	2	0.111	Up	0.429	0.933
GO:0051049	27	0.063	Up	0.430	0.933
GO:0032879	27	0.063	Up	0.430	0.933
GO:0019941	73	0.100	Down	0.432	0.933
GO:0043632	73	0.100	Down	0.432	0.933
GO:0043436	130	0.031	Down	0.433	0.933
GO:0006082	130	0.031	Down	0.433	0.933
GO:0071103	19	0.080	Down	0.434	0.933
GO:0006298	8	-0.010	Up	0.436	0.933
GO:0072330	21	0.041	Up	0.438	0.933
GO:0071897	1	NA	Up	0.441	0.933
GO:0051603	76	0.101	Down	0.443	0.933
GO:0044257	76	0.101	Down	0.443	0.933
GO:0030150	3	0.248	Down	0.450	0.933
GO:0006743	5	0.225	Up	0.451	0.933
GO:0006744	5	0.225	Up	0.451	0.933
GO:0072522	22	0.056	Up	0.451	0.933
GO:0046034	12	0.065	Up	0.455	0.933
GO:0043087	18	0.026	Up	0.461	0.933
GO:0033124	18	0.026	Up	0.461	0.933
GO:0051028	4	-0.095	Down	0.461	0.933
GO:0006468	91	0.023	Up	0.462	0.933
GO:0006402	7	0.067	Down	0.464	0.933
GO:0006536	5	-0.049	Down	0.466	0.933
GO:0008654	25	0.054	Up	0.468	0.933
GO:0010467	524	0.025	Down	0.469	0.933
GO:0006826	3	-0.097	Down	0.471	0.933
GO:0015684	3	-0.097	Down	0.471	0.933
GO:0010605	7	0.037	Down	0.471	0.933
GO:0007169	3	-0.100	Up	0.473	0.933
GO:0007167	3	-0.100	Up	0.473	0.933
GO:0016071	100	0.047	Down	0.475	0.933
GO:0019222	152	0.017	Down	0.476	0.933
GO:0009219	2	-0.309	Up	0.477	0.933
GO:0006629	86	0.026	Up	0.478	0.933
GO:0006767	8	0.161	Up	0.480	0.933
GO:0006766	8	0.161	Up	0.480	0.933
GO:0042364	8	0.161	Up	0.480	0.933
GO:0009110	8	0.161	Up	0.480	0.933
GO:0006413	48	0.006	Down	0.483	0.933
GO:0007067	11	0.140	Up	0.483	0.933
GO:0051674	10	0.009	Up	0.486	0.933
GO:0048870	10	0.009	Up	0.486	0.933
GO:0071824	11	0.141	Down	0.486	0.933
GO:0065004	11	0.141	Down	0.486	0.933
GO:0009084	3	0.093	Down	0.487	0.933
GO:0044699	809	0.021	Down	0.488	0.933
GO:0006633	19	0.038	Up	0.488	0.933
GO:0017038	19	0.000	Down	0.489	0.933
GO:0006914	6	-0.061	Down	0.489	0.933
GO:0006873	11	0.128	Up	0.490	0.933
GO:0030003	11	0.128	Up	0.490	0.933
GO:0044262	11	0.123	Down	0.493	0.933
GO:0006269	2	0.100	Up	0.493	0.933
GO:0020027	7	0.159	Up	0.494	0.933
GO:0042540	7	0.159	Up	0.494	0.933
GO:0006434	3	0.129	Down	0.496	0.933
GO:0008652	20	0.010	Down	0.503	0.933
GO:0016226	4	-0.007	Up	0.504	0.933
GO:0031163	4	-0.007	Up	0.504	0.933
GO:0051169	25	0.063	Down	0.504	0.933
GO:0006913	25	0.063	Down	0.504	0.933
GO:0006401	10	0.119	Down	0.507	0.933
GO:0009263	4	0.060	Up	0.511	0.933
GO:0031326	111	0.013	Down	0.511	0.933
GO:0009889	111	0.013	Down	0.511	0.933
GO:0044265	97	0.090	Down	0.511	0.933
GO:0032508	6	0.101	Down	0.513	0.933
GO:0032392	6	0.101	Down	0.513	0.933
GO:0006787	2	-0.282	Down	0.515	0.933
GO:0033015	2	-0.282	Down	0.515	0.933
GO:0051726	29	0.021	Up	0.516	0.933
GO:0032318	15	0.019	Up	0.517	0.933
GO:0033554	55	0.007	Up	0.518	0.933
GO:1901700	3	0.176	Up	0.521	0.933
GO:0010035	3	0.176	Up	0.521	0.933
GO:0000302	3	0.176	Up	0.521	0.933
GO:0009451	43	0.048	Up	0.522	0.933
GO:0044255	73	0.026	Up	0.528	0.933
GO:0006397	93	0.046	Down	0.528	0.933
GO:0006091	41	0.088	Down	0.530	0.933
GO:0006733	15	0.083	Down	0.530	0.933
GO:0010556	110	0.012	Down	0.530	0.933
GO:2000112	110	0.012	Down	0.530	0.933
GO:0061024	17	0.014	Down	0.531	0.933
GO:0043412	249	0.028	Up	0.532	0.933
GO:0009057	101	0.085	Down	0.533	0.933
GO:0006284	4	0.026	Down	0.534	0.933
GO:0043604	5	-0.080	Up	0.535	0.933
GO:0015893	3	-0.121	Up	0.538	0.933
GO:0006855	3	-0.121	Up	0.538	0.933
GO:0015749	2	0.432	Up	0.541	0.933
GO:0008645	2	0.432	Up	0.541	0.933
GO:0044238	1268	0.022	Down	0.542	0.933
GO:0040029	3	-0.093	Down	0.543	0.933
GO:0016310	99	0.023	Up	0.544	0.933
GO:0018205	6	-0.001	Up	0.544	0.933
GO:0006400	19	0.061	Up	0.545	0.933
GO:0044417	4	0.361	Up	0.547	0.933
GO:0042000	4	0.361	Up	0.547	0.933
GO:0051836	4	0.361	Up	0.547	0.933
GO:0044766	4	0.361	Up	0.547	0.933
GO:1902579	4	0.361	Up	0.547	0.933
GO:0051808	4	0.361	Up	0.547	0.933
GO:0044053	4	0.361	Up	0.547	0.933
GO:0040011	58	0.048	Up	0.548	0.933
GO:0044260	985	0.022	Down	0.548	0.933
GO:0016042	5	-0.029	Up	0.549	0.933
GO:0006541	2	-0.079	Down	0.550	0.933
GO:0080090	141	0.015	Down	0.552	0.933
GO:0000387	4	-0.006	Down	0.557	0.933
GO:0044248	137	0.072	Down	0.559	0.933
GO:0044267	562	0.033	Down	0.560	0.933
GO:0006732	37	0.033	Up	0.562	0.933
GO:0090305	10	0.026	Up	0.562	0.933
GO:0048522	8	0.064	Down	0.565	0.933
GO:0030163	86	0.091	Down	0.565	0.933
GO:0045047	7	0.038	Down	0.566	0.933
GO:0072599	7	0.038	Down	0.566	0.933
GO:0006612	7	0.038	Down	0.566	0.933
GO:0006396	207	0.034	Down	0.566	0.933
GO:0055082	12	0.110	Up	0.571	0.933
GO:1901606	6	-0.064	Up	0.572	0.933
GO:0009063	6	-0.064	Up	0.572	0.933
GO:0031325	4	0.010	Down	0.572	0.933
GO:0009893	4	0.010	Down	0.572	0.933
GO:0010604	4	0.010	Down	0.572	0.933
GO:0006268	2	0.218	Down	0.572	0.933
GO:0051052	4	-0.010	Up	0.575	0.933
GO:0006370	3	0.073	Down	0.576	0.933
GO:0044802	14	0.013	Down	0.576	0.933
GO:0008295	3	-0.086	Up	0.577	0.933
GO:0042401	3	-0.086	Up	0.577	0.933
GO:0009309	3	-0.086	Up	0.577	0.933
GO:0006596	3	-0.086	Up	0.577	0.933
GO:0006261	27	0.042	Up	0.583	0.933
GO:1901564	179	0.034	Down	0.583	0.933
GO:0006366	21	0.080	Up	0.584	0.933
GO:0006376	3	0.060	Down	0.584	0.933
GO:0043170	1043	0.021	Down	0.584	0.933
GO:0009069	7	0.031	Up	0.585	0.933
GO:0044237	1238	0.022	Down	0.586	0.933
GO:0050790	27	0.035	Up	0.587	0.933
GO:0065009	27	0.035	Up	0.587	0.933
GO:0042775	2	0.311	Up	0.591	0.933
GO:0006122	2	0.311	Up	0.591	0.933
GO:0007018	19	0.032	Down	0.592	0.933
GO:0055076	3	0.178	Up	0.592	0.933
GO:0046916	3	0.178	Up	0.592	0.933
GO:0007166	8	-0.035	Up	0.593	0.933
GO:0006323	10	0.048	Down	0.594	0.933
GO:0030522	2	-0.191	Down	0.599	0.933
GO:0009163	22	0.044	Up	0.599	0.933
GO:0042455	22	0.044	Up	0.599	0.933
GO:0015718	7	-0.033	Down	0.599	0.933
GO:0000290	3	0.026	Down	0.599	0.933
GO:0000288	3	0.026	Down	0.599	0.933
GO:0032787	53	0.032	Down	0.602	0.933
GO:0043244	3	-0.165	Down	0.604	0.933
GO:1901565	31	0.037	Down	0.606	0.933
GO:0009071	3	-0.068	Up	0.606	0.933
GO:0006546	3	-0.068	Up	0.606	0.933
GO:0031667	4	0.159	Down	0.608	0.933
GO:0007010	21	0.008	Up	0.608	0.933
GO:0017183	5	0.054	Up	0.610	0.933
GO:0017182	5	0.054	Up	0.610	0.933
GO:0033121	19	0.026	Up	0.610	0.933
GO:0030811	19	0.026	Up	0.610	0.933
GO:1900542	19	0.026	Up	0.610	0.933
GO:0009118	19	0.026	Up	0.610	0.933
GO:0006140	19	0.026	Up	0.610	0.933
GO:0031329	19	0.026	Up	0.610	0.933
GO:0019538	628	0.030	Down	0.611	0.933
GO:0043161	21	0.036	Up	0.612	0.933
GO:0010498	21	0.036	Up	0.612	0.933
GO:0044281	231	0.036	Down	0.612	0.933
GO:0070925	15	0.048	Down	0.613	0.933
GO:0009987	1474	0.020	Down	0.613	0.933
GO:0015672	24	0.045	Up	0.615	0.933
GO:0030258	4	-0.121	Down	0.615	0.933
GO:0042558	7	0.005	Down	0.616	0.933
GO:0006259	120	0.019	Up	0.617	0.933
GO:0006512	5	0.079	Down	0.617	0.933
GO:0006508	138	0.051	Down	0.617	0.933
GO:0071704	1299	0.022	Down	0.617	0.933
GO:0006352	14	0.065	Up	0.620	0.933
GO:0010876	9	-0.027	Down	0.621	0.933
GO:0006869	9	-0.027	Down	0.621	0.933
GO:0052192	54	0.044	Up	0.622	0.933
GO:0052126	54	0.044	Up	0.622	0.933
GO:0048878	14	0.123	Up	0.622	0.933
GO:0015748	6	0.082	Down	0.622	0.933
GO:0006950	91	0.011	Down	0.623	0.933
GO:0009233	2	-0.158	Up	0.625	0.933
GO:0009234	2	-0.158	Up	0.625	0.933
GO:0006302	5	-0.041	Up	0.626	0.933
GO:0051806	42	0.056	Up	0.629	0.933
GO:0030260	42	0.056	Up	0.629	0.933
GO:0009167	17	0.073	Up	0.630	0.933
GO:0009126	17	0.073	Up	0.630	0.933
GO:0042723	4	0.158	Up	0.631	0.933
GO:0006772	4	0.158	Up	0.631	0.933
GO:0042724	4	0.158	Up	0.631	0.933
GO:0009228	4	0.158	Up	0.631	0.933
GO:0033036	161	0.025	Down	0.631	0.933
GO:0009262	7	0.011	Up	0.631	0.933
GO:0046777	1	NA	Up	0.632	0.933
GO:0006289	11	0.029	Up	0.632	0.933
GO:0019439	37	0.087	Down	0.633	0.933
GO:0000027	8	0.197	Down	0.635	0.933
GO:0060627	23	0.065	Up	0.635	0.933
GO:1901135	97	0.054	Up	0.636	0.933
GO:0046700	39	0.080	Down	0.637	0.933
GO:0044270	39	0.080	Down	0.637	0.933
GO:1901361	39	0.080	Down	0.637	0.933
GO:0043038	40	0.077	Down	0.637	0.933
GO:0043039	40	0.077	Down	0.637	0.933
GO:0036211	206	0.032	Up	0.638	0.933
GO:0006464	206	0.032	Up	0.638	0.933
GO:0098662	17	0.069	Up	0.638	0.933
GO:0098655	17	0.069	Up	0.638	0.933
GO:0098660	17	0.069	Up	0.638	0.933
GO:0055086	85	0.056	Down	0.641	0.936
GO:0016070	365	0.026	Down	0.642	0.936
GO:0034641	602	0.019	Down	0.645	0.939
GO:0006429	2	0.574	Down	0.648	0.942
GO:0090407	64	0.045	Up	0.649	0.942
GO:0015711	18	0.028	Down	0.650	0.942
GO:0006812	42	0.028	Up	0.653	0.943
GO:0032268	27	0.033	Down	0.656	0.943
GO:0051252	87	0.015	Down	0.659	0.943
GO:0009150	40	0.054	Up	0.661	0.943
GO:0016311	15	0.038	Down	0.663	0.943
GO:0034728	6	0.068	Down	0.663	0.943
GO:0006334	6	0.068	Down	0.663	0.943
GO:0034655	35	0.092	Down	0.670	0.943
GO:0000819	2	0.198	Down	0.670	0.943
GO:0000070	2	0.198	Down	0.670	0.943
GO:0051716	109	0.014	Up	0.671	0.943
GO:0006139	560	0.021	Down	0.673	0.943
GO:0006807	627	0.019	Down	0.674	0.943
GO:0008152	1383	0.022	Down	0.674	0.943
GO:0097428	1	NA	Down	0.675	0.943
GO:0016567	11	0.136	Down	0.676	0.943
GO:0018202	6	0.020	Up	0.676	0.943
GO:0009187	4	0.082	Down	0.677	0.943
GO:0051259	6	-0.037	Up	0.677	0.943
GO:0072523	19	0.092	Down	0.680	0.943
GO:0009164	19	0.092	Down	0.680	0.943
GO:1901658	19	0.092	Down	0.680	0.943
GO:0042454	19	0.092	Down	0.680	0.943
GO:0006152	19	0.092	Down	0.680	0.943
GO:0046130	19	0.092	Down	0.680	0.943
GO:0050801	12	0.127	Up	0.684	0.943
GO:0055080	12	0.127	Up	0.684	0.943
GO:1901136	23	0.093	Down	0.684	0.943
GO:0048193	26	0.113	Up	0.685	0.943
GO:1901659	23	0.044	Up	0.687	0.943
GO:0009064	9	0.038	Down	0.687	0.943
GO:0006886	102	0.038	Down	0.691	0.943
GO:0019693	42	0.047	Up	0.694	0.943
GO:0048856	4	0.051	Up	0.696	0.943
GO:0045184	143	0.030	Down	0.698	0.943
GO:1902578	203	0.023	Up	0.698	0.943
GO:0006412	231	0.049	Down	0.699	0.943
GO:0009259	41	0.050	Up	0.699	0.943
GO:0017004	2	-0.476	Up	0.699	0.943
GO:0009394	3	-0.174	Down	0.699	0.943
GO:0019692	3	-0.174	Down	0.699	0.943
GO:0009200	3	-0.174	Down	0.699	0.943
GO:1902600	16	0.077	Up	0.700	0.943
GO:0051828	46	0.051	Up	0.701	0.943
GO:0044409	46	0.051	Up	0.701	0.943
GO:0090304	471	0.021	Down	0.702	0.943
GO:0051649	138	0.031	Down	0.703	0.943
GO:0031323	139	0.014	Down	0.703	0.943
GO:0071705	16	0.025	Down	0.704	0.943
GO:0009123	18	0.065	Up	0.705	0.943
GO:0009161	18	0.065	Up	0.705	0.943
GO:0009072	3	-0.026	Up	0.707	0.943
GO:0009073	3	-0.026	Up	0.707	0.943
GO:0000724	2	-0.302	Down	0.707	0.943
GO:0000725	2	-0.302	Down	0.707	0.943
GO:0032259	26	0.038	Down	0.708	0.943
GO:0032446	18	0.084	Down	0.708	0.943
GO:0009186	4	0.178	Up	0.711	0.943
GO:0051336	21	0.038	Up	0.712	0.943
GO:0055085	69	0.036	Up	0.712	0.943
GO:0015031	142	0.031	Down	0.714	0.943
GO:0016570	11	0.012	Down	0.714	0.943
GO:0016569	11	0.012	Down	0.714	0.943
GO:0008104	148	0.028	Down	0.715	0.943
GO:0006220	8	-0.050	Up	0.719	0.943
GO:0006432	3	-0.180	Up	0.720	0.943
GO:0022406	4	0.070	Down	0.720	0.943
GO:0048278	4	0.070	Down	0.720	0.943
GO:0006904	4	0.070	Down	0.720	0.943
GO:0009154	18	0.086	Down	0.723	0.943
GO:0006195	18	0.086	Down	0.723	0.943
GO:0009261	18	0.086	Down	0.723	0.943
GO:0046483	584	0.020	Down	0.724	0.943
GO:0006725	583	0.020	Down	0.726	0.943
GO:0006270	11	0.076	Up	0.726	0.943
GO:0000041	7	0.073	Up	0.729	0.943
GO:0016192	83	0.048	Up	0.729	0.943
GO:0009205	30	0.069	Up	0.730	0.943
GO:0009199	30	0.069	Up	0.730	0.943
GO:0009190	3	0.024	Down	0.731	0.943
GO:1901360	587	0.020	Down	0.732	0.943
GO:0009067	3	-0.043	Down	0.733	0.943
GO:0008283	3	-0.043	Up	0.733	0.943
GO:0044765	199	0.023	Up	0.734	0.943
GO:0051168	8	0.039	Down	0.737	0.943
GO:0002377	3	0.244	Up	0.739	0.943
GO:0002440	3	0.244	Up	0.739	0.943
GO:0000304	2	0.403	Up	0.740	0.943
GO:0006383	7	0.013	Down	0.740	0.943
GO:0015988	14	0.088	Up	0.741	0.943
GO:0015991	14	0.088	Up	0.741	0.943
GO:0034660	124	0.027	Down	0.741	0.943
GO:0009070	2	0.280	Up	0.744	0.943
GO:0070727	106	0.036	Down	0.746	0.943
GO:0034613	106	0.036	Down	0.746	0.943
GO:0048583	27	0.046	Down	0.746	0.943
GO:0043414	18	0.015	Down	0.748	0.943
GO:0046907	134	0.031	Down	0.749	0.943
GO:0051641	142	0.030	Down	0.749	0.943
GO:2001141	85	0.015	Down	0.752	0.943
GO:0006355	85	0.015	Down	0.752	0.943
GO:0044283	59	0.020	Up	0.755	0.943
GO:1901069	17	0.078	Down	0.755	0.943
GO:0006184	17	0.078	Down	0.755	0.943
GO:0009146	17	0.078	Down	0.755	0.943
GO:0009207	17	0.078	Down	0.755	0.943
GO:0009203	17	0.078	Down	0.755	0.943
GO:0006333	12	0.129	Down	0.760	0.947
GO:0071702	174	0.026	Down	0.761	0.947
GO:0006165	2	-0.161	Up	0.762	0.947
GO:0046939	2	-0.161	Up	0.762	0.947
GO:0048519	16	0.002	Down	0.766	0.950
GO:0006470	11	0.055	Up	0.769	0.953
GO:0006865	4	0.095	Up	0.773	0.954
GO:0052652	2	-0.286	Down	0.773	0.954
GO:0046068	2	-0.286	Down	0.773	0.954
GO:0006418	38	0.080	Down	0.775	0.955
GO:0006399	78	0.026	Up	0.776	0.955
GO:0050793	4	0.138	Up	0.776	0.955
GO:0009141	34	0.076	Up	0.778	0.955
GO:0046486	25	0.011	Up	0.779	0.956
GO:0045454	29	0.030	Down	0.783	0.957
GO:0090501	4	-0.046	Down	0.784	0.957
GO:0006793	226	0.030	Up	0.785	0.957
GO:0042147	3	0.024	Down	0.785	0.957
GO:0016197	3	0.024	Down	0.785	0.957
GO:0006072	5	0.123	Down	0.789	0.960
GO:0009117	71	0.059	Down	0.790	0.960
GO:0009166	19	0.097	Down	0.792	0.960
GO:0060249	3	0.160	Down	0.795	0.960
GO:0000723	3	0.160	Down	0.795	0.960
GO:0032200	3	0.160	Down	0.795	0.960
GO:0006891	3	-0.084	Up	0.796	0.960
GO:0048285	14	0.094	Up	0.797	0.960
GO:0000280	14	0.094	Up	0.797	0.960
GO:0009894	22	0.023	Down	0.798	0.960
GO:1902589	44	0.028	Down	0.800	0.961
GO:0006644	35	0.023	Up	0.806	0.967
GO:0031497	7	0.054	Down	0.808	0.967
GO:0015849	13	0.001	Down	0.809	0.967
GO:0046942	13	0.001	Down	0.809	0.967
GO:0006310	18	-0.028	Down	0.810	0.967
GO:0046785	3	0.152	Up	0.812	0.967
GO:0031109	3	0.152	Up	0.812	0.967
GO:0007020	3	0.152	Up	0.812	0.967
GO:0042274	9	0.094	Down	0.814	0.967
GO:1901566	80	0.036	Up	0.817	0.967
GO:0046434	22	0.113	Down	0.818	0.967
GO:0006351	81	0.026	Down	0.818	0.967
GO:0006836	1	NA	Down	0.818	0.967
GO:0044711	147	0.033	Up	0.819	0.967
GO:0009143	18	0.098	Down	0.820	0.967
GO:0006753	73	0.062	Down	0.821	0.967
GO:0006446	9	0.069	Up	0.823	0.967
GO:0016114	2	0.257	Down	0.826	0.967
GO:0006721	2	0.257	Down	0.826	0.967
GO:0006424	3	0.051	Up	0.826	0.967
GO:0001510	9	0.043	Up	0.827	0.967
GO:0006611	3	0.275	Up	0.827	0.967
GO:0019673	3	0.232	Down	0.830	0.967
GO:0015992	19	0.081	Up	0.830	0.967
GO:0006818	19	0.081	Up	0.830	0.967
GO:0006119	3	-0.115	Down	0.831	0.967
GO:0042773	3	-0.115	Down	0.831	0.967
GO:0046488	18	0.016	Up	0.833	0.968
GO:0019637	115	0.050	Down	0.836	0.968
GO:0044249	516	0.021	Up	0.837	0.968
GO:0042255	11	0.072	Down	0.837	0.968
GO:0032774	84	0.028	Down	0.838	0.968
GO:0006040	4	0.057	Up	0.838	0.968
GO:0006163	43	0.059	Up	0.841	0.970
GO:0016925	4	0.106	Down	0.843	0.971
GO:1901292	20	0.114	Down	0.845	0.972
GO:0006360	3	0.190	Down	0.847	0.972
GO:1901071	3	0.049	Down	0.848	0.972
GO:0009144	31	0.073	Up	0.849	0.972
GO:0046128	41	0.073	Up	0.851	0.972
GO:0042278	41	0.073	Up	0.851	0.972
GO:0044763	585	0.023	Up	0.853	0.972
GO:0055067	8	0.183	Down	0.864	0.972
GO:0006885	8	0.183	Down	0.864	0.972
GO:0035556	36	0.034	Down	0.864	0.972
GO:0007033	4	0.122	Down	0.865	0.972
GO:0006471	3	0.143	Up	0.865	0.972
GO:0055114	95	0.056	Up	0.865	0.972
GO:0018193	25	0.040	Up	0.866	0.972
GO:1901657	48	0.057	Down	0.866	0.972
GO:1902582	80	0.029	Down	0.866	0.972
GO:0034654	128	0.024	Down	0.869	0.972
GO:0070271	42	0.055	Down	0.869	0.972
GO:0006461	42	0.055	Down	0.869	0.972
GO:0071822	51	0.038	Down	0.873	0.972
GO:0022900	7	0.021	Up	0.874	0.972
GO:1901293	37	0.051	Up	0.875	0.972
GO:0007264	24	0.074	Down	0.876	0.972
GO:0009058	529	0.022	Up	0.877	0.972
GO:0072528	14	0.034	Down	0.877	0.972
GO:0006928	33	0.010	Down	0.880	0.972
GO:0007154	59	0.021	Down	0.882	0.972
GO:0019725	42	0.044	Up	0.882	0.972
GO:0051171	110	0.013	Down	0.886	0.972
GO:0019219	110	0.013	Down	0.886	0.972
GO:0045851	7	0.193	Up	0.887	0.972
GO:0030641	7	0.193	Up	0.887	0.972
GO:0051452	7	0.193	Up	0.887	0.972
GO:0007035	7	0.193	Up	0.887	0.972
GO:0051453	7	0.193	Up	0.887	0.972
GO:0030004	7	0.193	Up	0.887	0.972
GO:0009165	36	0.052	Up	0.888	0.972
GO:0010639	3	-0.208	Down	0.888	0.972
GO:0051129	3	-0.208	Down	0.888	0.972
GO:0030837	3	-0.208	Down	0.888	0.972
GO:0051494	3	-0.208	Down	0.888	0.972
GO:0032272	3	-0.208	Down	0.888	0.972
GO:0031333	3	-0.208	Down	0.888	0.972
GO:0006650	24	0.010	Up	0.890	0.974
GO:0043623	26	0.067	Down	0.891	0.974
GO:0070972	8	0.007	Down	0.893	0.974
GO:0051179	346	0.022	Up	0.894	0.974
GO:0000393	5	-0.050	Down	0.896	0.974
GO:0006796	219	0.029	Up	0.896	0.974
GO:0052646	6	0.105	Up	0.897	0.974
GO:0009225	4	0.289	Up	0.901	0.974
GO:0034637	3	0.216	Down	0.903	0.974
GO:0023052	54	0.022	Up	0.904	0.974
GO:0044700	54	0.022	Up	0.904	0.974
GO:0007165	54	0.022	Up	0.904	0.974
GO:0008216	4	-0.019	Down	0.905	0.974
GO:0006595	4	-0.019	Down	0.905	0.974
GO:0043085	4	0.072	Down	0.906	0.974
GO:0044093	4	0.072	Down	0.906	0.974
GO:0022603	2	0.407	Up	0.907	0.974
GO:0009116	47	0.059	Down	0.909	0.975
GO:0015908	3	-0.064	Up	0.911	0.975
GO:1901576	518	0.021	Up	0.911	0.975
GO:0008299	7	0.180	Down	0.912	0.975
GO:0006720	7	0.180	Down	0.912	0.975
GO:0051187	3	-0.184	Down	0.914	0.975
GO:1901068	19	0.089	Down	0.915	0.975
GO:0007017	31	0.014	Up	0.917	0.977
GO:0034220	19	0.054	Up	0.918	0.977
GO:0046578	17	0.024	Down	0.925	0.981
GO:0051056	17	0.024	Down	0.925	0.981
GO:1902531	17	0.024	Down	0.925	0.981
GO:0042592	47	0.050	Up	0.927	0.982
GO:0006810	332	0.022	Up	0.928	0.982
GO:0006405	4	-0.021	Down	0.929	0.982
GO:0006749	4	-0.192	Up	0.933	0.984
GO:0046394	39	0.019	Up	0.935	0.984
GO:0016053	39	0.019	Up	0.935	0.984
GO:0044271	158	0.022	Up	0.936	0.984
GO:0051234	333	0.022	Up	0.936	0.984
GO:0006613	5	0.072	Down	0.941	0.987
GO:0006614	5	0.072	Down	0.941	0.987
GO:0006811	79	0.016	Down	0.947	0.987
GO:0006606	10	0.072	Down	0.947	0.987
GO:0051170	10	0.072	Down	0.947	0.987
GO:0034504	10	0.072	Down	0.947	0.987
GO:1902593	10	0.072	Down	0.947	0.987
GO:0044744	10	0.072	Down	0.947	0.987
GO:0032313	13	0.010	Down	0.949	0.987
GO:0032483	13	0.010	Down	0.949	0.987
GO:0015931	11	-0.004	Down	0.957	0.990
GO:0042819	3	0.426	Up	0.958	0.990
GO:0042816	3	0.426	Up	0.958	0.990
GO:0008614	3	0.426	Up	0.958	0.990
GO:0022904	6	0.021	Up	0.959	0.990
GO:0032270	3	0.033	Up	0.959	0.990
GO:0051247	3	0.033	Up	0.959	0.990
GO:0072525	4	0.278	Down	0.961	0.990
GO:0034470	83	0.034	Down	0.965	0.990
GO:0072521	48	0.067	Up	0.967	0.990
GO:0044710	420	0.031	Down	0.967	0.990
GO:0019438	148	0.021	Up	0.969	0.990
GO:0030048	4	-0.016	Up	0.969	0.990
GO:0016458	3	0.047	Down	0.970	0.990
GO:0009059	385	0.023	Up	0.971	0.990
GO:0072511	6	0.042	Down	0.972	0.990
GO:0070838	6	0.042	Down	0.972	0.990
GO:0010646	21	0.044	Up	0.973	0.990
GO:0023051	21	0.044	Up	0.973	0.990
GO:0009966	21	0.044	Up	0.973	0.990
GO:0034645	383	0.023	Up	0.974	0.990
GO:0009119	46	0.058	Down	0.976	0.991
GO:0006308	4	0.116	Up	0.979	0.993
GO:0018130	152	0.021	Down	0.980	0.993
GO:0072527	15	0.036	Up	0.981	0.993
GO:0046039	18	0.083	Down	0.982	0.993
GO:0007034	5	-0.026	Down	0.993	0.999
GO:0006607	3	0.251	Down	0.994	0.999
GO:0046903	5	0.083	Up	0.994	0.999
GO:0006887	5	0.083	Up	0.994	0.999
GO:0032940	5	0.083	Up	0.994	0.999
GO:0006888	20	0.145	Up	0.995	0.999
GO:0043952	5	0.103	Down	0.995	0.999
GO:0006221	7	-0.052	Up	0.995	0.999
GO:0009432	2	0.344	Down	0.998	0.999
GO:0000096	3	0.136	Up	0.998	0.999
GO:1901362	155	0.021	Up	0.999	0.999

Now KEGG pathway enrichment again making use of mroast and camera.

indices <- ids2indices(kegg.gene.sets, rownames(v2))
keg_mr <- mroast(v2, index = indices, design = modRUV, contrast = 2, nrot = 10000, set.statistic = "floormean")
keg_cam <- camera(v2, index = indices, design = modRUV, contrast = 2)
kable(keg_mr, digits = 3)

	NGenes	PropDown	PropUp	Direction	PValue	FDR	PValue.Mixed	FDR.Mixed
ec00250__PK__KEGG	12	0.250	0.000	Down	0.003	0.098	0.013	0.028
ec00740__PK__KEGG	8	0.375	0.500	Up	0.004	0.098	0.000	0.015
ec00710__PK__KEGG	10	0.600	0.000	Down	0.004	0.098	0.006	0.020
ec00280__PK__KEGG	8	0.125	0.500	Up	0.004	0.098	0.005	0.018
ec00600__PK__KEGG	11	0.091	0.545	Up	0.005	0.098	0.004	0.017
ec00650__PK__KEGG	18	0.056	0.444	Up	0.006	0.098	0.009	0.024
ec00010__PK__KEGG	25	0.440	0.080	Down	0.007	0.098	0.004	0.017
ec00562__PK__KEGG	18	0.278	0.111	Down	0.009	0.098	0.006	0.020
ec00020__PK__KEGG	18	0.111	0.389	Up	0.009	0.098	0.002	0.015
ec00380__PK__KEGG	61	0.180	0.246	Up	0.009	0.098	0.002	0.015
ec00565__PK__KEGG	24	0.208	0.292	Up	0.012	0.100	0.001	0.015
ec00561__PK__KEGG	15	0.133	0.200	Up	0.013	0.100	0.004	0.017
ec00591__PK__KEGG	7	0.286	0.143	Down	0.014	0.100	0.003	0.017
ec00230__PK__KEGG	78	0.244	0.128	Down	0.014	0.100	0.001	0.015
ec00720__PK__KEGG	17	0.118	0.412	Up	0.018	0.100	0.009	0.023
ec00900__PK__KEGG	26	0.077	0.269	Up	0.019	0.100	0.007	0.022
ec00030__PK__KEGG	14	0.429	0.000	Down	0.019	0.100	0.026	0.043
ec00983__PK__KEGG	15	0.400	0.067	Down	0.020	0.100	0.012	0.027
ec00590__PK__KEGG	7	0.286	0.000	Down	0.021	0.100	0.011	0.026
ec00361__PK__KEGG	6	0.167	0.500	Up	0.022	0.100	0.011	0.026
ec00362__PK__KEGG	19	0.158	0.368	Up	0.024	0.100	0.016	0.031
ec00440__PK__KEGG	4	0.500	0.000	Down	0.026	0.100	0.026	0.043
ec00624__PK__KEGG	36	0.222	0.222	Up	0.028	0.100	0.001	0.015
ec00240__PK__KEGG	72	0.194	0.167	Up	0.029	0.100	0.001	0.015
ec00627__PK__KEGG	61	0.213	0.246	Up	0.029	0.100	0.002	0.015
ec00351__PK__KEGG	1	0.000	1.000	Up	0.030	0.100	0.030	0.047
ec00730__PK__KEGG	14	0.071	0.214	Up	0.030	0.100	0.042	0.063
ec00660__PK__KEGG	3	0.000	0.667	Up	0.031	0.100	0.033	0.051
ec00625__PK__KEGG	4	0.250	0.250	Down	0.032	0.100	0.023	0.041
ec00623__PK__KEGG	17	0.118	0.353	Up	0.034	0.100	0.012	0.026
ec00062__PK__KEGG	6	0.167	0.667	Up	0.034	0.100	0.016	0.031
ec00860__PK__KEGG	50	0.160	0.200	Up	0.034	0.100	0.011	0.026
ec00970__PK__KEGG	41	0.341	0.171	Down	0.035	0.100	0.007	0.022
ec00360__PK__KEGG	49	0.204	0.245	Up	0.036	0.100	0.001	0.015
ec00942__PK__KEGG	46	0.174	0.261	Up	0.038	0.100	0.004	0.018
ec00941__PK__KEGG	36	0.222	0.222	Up	0.038	0.100	0.001	0.015
ec00945__PK__KEGG	36	0.222	0.222	Up	0.038	0.100	0.002	0.015
ec00270__PK__KEGG	49	0.224	0.204	Up	0.039	0.100	0.002	0.015
ec01057__PK__KEGG	42	0.190	0.238	Up	0.039	0.100	0.004	0.017
ec00053__PK__KEGG	7	0.143	0.286	Up	0.039	0.100	0.005	0.018
ec01051__PK__KEGG	36	0.222	0.222	Up	0.040	0.100	0.002	0.015
ec00260__PK__KEGG	16	0.062	0.438	Up	0.040	0.100	0.021	0.039
ec00253__PK__KEGG	51	0.176	0.235	Up	0.040	0.100	0.004	0.017
ec00130__PK__KEGG	40	0.225	0.200	Up	0.041	0.100	0.002	0.015
ec00340__PK__KEGG	46	0.196	0.239	Up	0.041	0.100	0.003	0.017
ec00920__PK__KEGG	4	0.000	0.500	Up	0.042	0.100	0.066	0.087
ec00350__PK__KEGG	50	0.200	0.220	Up	0.044	0.101	0.003	0.015
ec00450__PK__KEGG	41	0.195	0.220	Up	0.045	0.101	0.002	0.015
ec00940__PK__KEGG	48	0.188	0.229	Up	0.047	0.103	0.002	0.015
ec00981__PK__KEGG	38	0.184	0.237	Up	0.048	0.103	0.005	0.018
ec00903__PK__KEGG	16	0.188	0.312	Up	0.048	0.103	0.016	0.031
ec00965__PK__KEGG	12	0.083	0.417	Up	0.055	0.114	0.049	0.072
ec00480__PK__KEGG	25	0.200	0.280	Up	0.056	0.114	0.002	0.015
ec00910__PK__KEGG	6	0.167	0.000	Down	0.057	0.114	0.078	0.094
ec00564__PK__KEGG	53	0.151	0.264	Up	0.058	0.114	0.008	0.022
ec00310__PK__KEGG	40	0.225	0.275	Up	0.061	0.114	0.005	0.018
ec00603__PK__KEGG	1	0.000	1.000	Up	0.061	0.114	0.061	0.087
ec00592__PK__KEGG	9	0.222	0.222	Down	0.063	0.114	0.006	0.020
ec00522__PK__KEGG	1	0.000	1.000	Up	0.064	0.114	0.064	0.087
ec00513__PK__KEGG	1	0.000	1.000	Up	0.064	0.114	0.064	0.087
ec00944__PK__KEGG	1	0.000	1.000	Up	0.064	0.114	0.064	0.087
ec00604__PK__KEGG	1	0.000	1.000	Up	0.065	0.114	0.065	0.087
ec00512__PK__KEGG	1	0.000	1.000	Up	0.068	0.115	0.068	0.087
ec00906__PK__KEGG	13	0.154	0.385	Up	0.068	0.115	0.016	0.031
ec00601__PK__KEGG	1	0.000	1.000	Up	0.069	0.115	0.069	0.087
ec00626__PK__KEGG	13	0.154	0.308	Up	0.076	0.125	0.030	0.047
ec00982__PK__KEGG	3	0.333	0.333	Down	0.077	0.125	0.039	0.059
ec00630__PK__KEGG	9	0.111	0.444	Up	0.080	0.127	0.013	0.029
ec00680__PK__KEGG	24	0.208	0.292	Up	0.082	0.127	0.010	0.024
ec00950__PK__KEGG	48	0.167	0.229	Up	0.083	0.127	0.009	0.023
ec00330__PK__KEGG	27	0.074	0.296	Up	0.084	0.127	0.014	0.029
ec00966__PK__KEGG	3	0.333	0.333	Down	0.085	0.127	0.027	0.044
ec00140__PK__KEGG	3	0.333	0.333	Down	0.086	0.127	0.025	0.042
ec00540__PK__KEGG	11	0.091	0.364	Up	0.086	0.127	0.077	0.094
ec00300__PK__KEGG	19	0.158	0.211	Up	0.088	0.128	0.021	0.039
ec00622__PK__KEGG	4	0.250	0.500	Up	0.092	0.131	0.009	0.023
ec00231__PK__KEGG	11	0.091	0.364	Up	0.093	0.131	0.057	0.083
ec00930__PK__KEGG	7	0.143	0.429	Up	0.098	0.136	0.105	0.125
ec00790__PK__KEGG	9	0.222	0.222	Down	0.100	0.137	0.004	0.017
ec00770__PK__KEGG	8	0.000	0.250	Up	0.102	0.137	0.124	0.143
ec00904__PK__KEGG	12	0.167	0.333	Up	0.104	0.137	0.024	0.042
ec00071__PK__KEGG	18	0.278	0.333	Up	0.105	0.137	0.022	0.040
ec00281__PK__KEGG	4	0.250	0.500	Up	0.105	0.137	0.067	0.087
ec00670__PK__KEGG	7	0.000	0.429	Up	0.105	0.137	0.138	0.156
ec00642__PK__KEGG	13	0.154	0.308	Up	0.107	0.137	0.067	0.087
ec00785__PK__KEGG	2	0.000	0.500	Up	0.110	0.140	0.166	0.185
ec00640__PK__KEGG	17	0.118	0.294	Up	0.145	0.181	0.008	0.022
ec00364__PK__KEGG	6	0.167	0.333	Up	0.146	0.181	0.111	0.130
ec00830__PK__KEGG	5	0.200	0.200	Down	0.149	0.183	0.022	0.040
ec00510__PK__KEGG	3	0.000	0.333	Up	0.156	0.187	0.228	0.246
ec00620__PK__KEGG	23	0.174	0.174	Up	0.158	0.187	0.009	0.023
ec00563__PK__KEGG	7	0.000	0.429	Up	0.158	0.187	0.187	0.205
ec00051__PK__KEGG	20	0.150	0.150	Down	0.171	0.201	0.016	0.031
ec00040__PK__KEGG	6	0.000	0.333	Up	0.187	0.217	0.329	0.341
ec00960__PK__KEGG	18	0.167	0.222	Up	0.229	0.262	0.063	0.087
ec00908__PK__KEGG	2	0.000	0.500	Up	0.233	0.264	0.074	0.092
ec00363__PK__KEGG	6	0.167	0.167	Down	0.237	0.266	0.034	0.052
ec00061__PK__KEGG	9	0.222	0.222	Up	0.262	0.291	0.079	0.094
ec01056__PK__KEGG	3	0.000	0.333	Up	0.284	0.312	0.418	0.426
ec00500__PK__KEGG	5	0.200	0.200	Down	0.297	0.323	0.127	0.145
ec00760__PK__KEGG	12	0.083	0.250	Up	0.300	0.324	0.153	0.172
ec00633__PK__KEGG	4	0.000	0.500	Up	0.308	0.329	0.283	0.299
ec00400__PK__KEGG	8	0.000	0.250	Up	0.315	0.333	0.461	0.465
ec00410__PK__KEGG	4	0.000	0.250	Down	0.350	0.367	0.074	0.092
ec00750__PK__KEGG	2	0.000	0.000	Up	0.455	0.472	0.406	0.418
ec00780__PK__KEGG	13	0.154	0.077	Up	0.511	0.526	0.194	0.212
ec00052__PK__KEGG	8	0.125	0.125	Down	0.580	0.591	0.281	0.299
ec00520__PK__KEGG	21	0.095	0.143	Down	0.586	0.591	0.303	0.318
ec00521__PK__KEGG	5	0.000	0.000	Down	0.606	0.606	0.840	0.840

Also test using limma’s camera

kable(keg_cam, digits = 3)

	NGenes	Correlation	Direction	PValue	FDR
ec00710__PK__KEGG	10	0.175	Down	0.054	0.882
ec00250__PK__KEGG	12	0.040	Down	0.065	0.882
ec00600__PK__KEGG	11	0.059	Up	0.074	0.882
ec00650__PK__KEGG	18	0.043	Up	0.107	0.882
ec00010__PK__KEGG	25	0.126	Down	0.128	0.882
ec00440__PK__KEGG	4	0.201	Down	0.137	0.882
ec00920__PK__KEGG	4	0.221	Up	0.171	0.882
ec00280__PK__KEGG	8	0.000	Up	0.173	0.882
ec00030__PK__KEGG	14	0.097	Down	0.173	0.882
ec00562__PK__KEGG	18	0.052	Down	0.190	0.882
ec00910__PK__KEGG	6	-0.038	Down	0.198	0.882
ec00351__PK__KEGG	1	NA	Up	0.204	0.882
ec00983__PK__KEGG	15	0.108	Down	0.210	0.882
ec00020__PK__KEGG	18	0.082	Up	0.216	0.882
ec00660__PK__KEGG	3	0.064	Up	0.219	0.882
ec00601__PK__KEGG	1	NA	Up	0.230	0.882
ec00944__PK__KEGG	1	NA	Up	0.230	0.882
ec00522__PK__KEGG	1	NA	Up	0.230	0.882
ec00513__PK__KEGG	1	NA	Up	0.230	0.882
ec00603__PK__KEGG	1	NA	Up	0.230	0.882
ec00604__PK__KEGG	1	NA	Up	0.230	0.882
ec00512__PK__KEGG	1	NA	Up	0.230	0.882
ec00900__PK__KEGG	26	0.099	Up	0.231	0.882
ec00720__PK__KEGG	17	0.056	Up	0.234	0.882
ec00730__PK__KEGG	14	0.029	Up	0.239	0.882
ec00260__PK__KEGG	16	0.048	Up	0.249	0.882
ec00361__PK__KEGG	6	0.029	Up	0.256	0.882
ec00590__PK__KEGG	7	0.040	Down	0.284	0.882
ec00965__PK__KEGG	12	0.093	Up	0.288	0.882
ec00362__PK__KEGG	19	0.010	Up	0.296	0.882
ec00510__PK__KEGG	3	-0.038	Up	0.297	0.882
ec00561__PK__KEGG	15	0.020	Up	0.305	0.882
ec00040__PK__KEGG	6	-0.035	Up	0.308	0.882
ec00062__PK__KEGG	6	0.067	Up	0.308	0.882
ec00670__PK__KEGG	7	0.114	Up	0.309	0.882
ec00785__PK__KEGG	2	-0.456	Up	0.311	0.882
ec00770__PK__KEGG	8	0.077	Up	0.327	0.882
ec00625__PK__KEGG	4	-0.116	Down	0.330	0.882
ec00930__PK__KEGG	7	-0.013	Up	0.333	0.882
ec00565__PK__KEGG	24	0.063	Up	0.337	0.882
ec00540__PK__KEGG	11	0.073	Up	0.356	0.882
ec00623__PK__KEGG	17	0.048	Up	0.357	0.882
ec01056__PK__KEGG	3	-0.091	Up	0.365	0.882
ec00563__PK__KEGG	7	0.116	Up	0.373	0.882
ec00860__PK__KEGG	50	0.044	Up	0.395	0.882
ec00591__PK__KEGG	7	-0.043	Down	0.403	0.882
ec00400__PK__KEGG	8	-0.031	Up	0.427	0.882
ec00740__PK__KEGG	8	0.088	Up	0.435	0.882
ec00380__PK__KEGG	61	0.026	Up	0.436	0.882
ec00231__PK__KEGG	11	0.006	Up	0.438	0.882
ec00364__PK__KEGG	6	-0.048	Up	0.453	0.882
ec00982__PK__KEGG	3	-0.186	Down	0.461	0.882
ec00942__PK__KEGG	46	0.066	Up	0.472	0.882
ec00642__PK__KEGG	13	0.042	Up	0.479	0.882
ec00633__PK__KEGG	4	0.271	Up	0.484	0.882
ec00903__PK__KEGG	16	0.015	Up	0.495	0.882
ec00906__PK__KEGG	13	0.077	Up	0.497	0.882
ec00281__PK__KEGG	4	-0.034	Up	0.507	0.882
ec00966__PK__KEGG	3	-0.138	Down	0.515	0.882
ec00140__PK__KEGG	3	-0.138	Down	0.515	0.882
ec00626__PK__KEGG	13	0.027	Up	0.515	0.882
ec00564__PK__KEGG	53	0.046	Up	0.518	0.882
ec00053__PK__KEGG	7	-0.010	Up	0.527	0.882
ec00253__PK__KEGG	51	0.042	Up	0.550	0.882
ec00760__PK__KEGG	12	0.155	Up	0.552	0.882
ec00630__PK__KEGG	9	0.063	Up	0.556	0.882
ec01057__PK__KEGG	42	0.053	Up	0.559	0.882
ec00750__PK__KEGG	2	0.114	Up	0.560	0.882
ec00981__PK__KEGG	38	0.057	Up	0.562	0.882
ec00970__PK__KEGG	41	0.062	Down	0.572	0.882
ec00230__PK__KEGG	78	0.031	Down	0.587	0.882
ec00627__PK__KEGG	61	0.060	Up	0.609	0.882
ec00340__PK__KEGG	46	0.059	Up	0.610	0.882
ec00940__PK__KEGG	48	0.062	Up	0.623	0.882
ec00904__PK__KEGG	12	0.058	Up	0.624	0.882
ec00330__PK__KEGG	27	0.032	Up	0.633	0.882
ec00350__PK__KEGG	50	0.047	Up	0.648	0.882
ec00950__PK__KEGG	48	0.053	Up	0.649	0.882
ec00521__PK__KEGG	5	0.123	Down	0.654	0.882
ec00360__PK__KEGG	49	0.053	Up	0.671	0.882
ec01051__PK__KEGG	36	0.058	Up	0.672	0.882
ec00061__PK__KEGG	9	0.175	Up	0.681	0.882
ec00071__PK__KEGG	18	0.031	Up	0.687	0.882
ec00450__PK__KEGG	41	0.061	Up	0.700	0.882
ec00624__PK__KEGG	36	0.050	Up	0.701	0.882
ec00830__PK__KEGG	5	0.011	Down	0.715	0.882
ec00941__PK__KEGG	36	0.055	Up	0.715	0.882
ec00945__PK__KEGG	36	0.055	Up	0.715	0.882
ec00908__PK__KEGG	2	0.056	Up	0.723	0.882
ec00300__PK__KEGG	19	0.007	Up	0.728	0.882
ec00310__PK__KEGG	40	0.023	Up	0.765	0.903
ec00500__PK__KEGG	5	0.069	Down	0.770	0.903
ec00480__PK__KEGG	25	0.052	Up	0.770	0.903
ec00960__PK__KEGG	18	0.058	Up	0.782	0.907
ec00240__PK__KEGG	72	0.021	Up	0.813	0.918
ec00130__PK__KEGG	40	0.048	Up	0.814	0.918
ec00640__PK__KEGG	17	0.029	Up	0.820	0.918
ec00780__PK__KEGG	13	0.044	Up	0.825	0.918
ec00622__PK__KEGG	4	-0.120	Up	0.838	0.923
ec00680__PK__KEGG	24	0.019	Up	0.867	0.926
ec00051__PK__KEGG	20	0.028	Down	0.870	0.926
ec00270__PK__KEGG	49	0.035	Up	0.873	0.926
ec00520__PK__KEGG	21	0.048	Down	0.875	0.926
ec00363__PK__KEGG	6	-0.018	Down	0.894	0.937
ec00790__PK__KEGG	9	0.041	Down	0.915	0.937
ec00410__PK__KEGG	4	0.037	Down	0.919	0.937
ec00620__PK__KEGG	23	0.059	Up	0.920	0.937
ec00052__PK__KEGG	8	0.043	Down	0.934	0.938
ec00592__PK__KEGG	9	-0.043	Down	0.938	0.938

Gene sets from Daily et al and Shock et al

We now test using roast and camera for deregulation of gene sets obtained from the papers:

Daily, J. P., D. Scanfeld, N. Pochet, K. Le Roch, D. Plouffe, M. Kamal, O. Sarr, et al. 2007. “Distinct Physiological States of Plasmodium Falciparum in Malaria-Infected Patients.” Nature 450 (7172): 1091–95.

Shock, Jennifer L., Kael F. Fischer, and Joseph L. DeRisi. 2007. “Whole-Genome Analysis of mRNA Decay in Plasmodium Falciparum Reveals a Global Lengthening of mRNA Half-Life during the Intra-Erythrocytic Development Cycle.” Genome Biology 8 (7): R134.

setwd(wd)

# Load gene lists from Daily et al and Shock et al
daily_figure2 <- fread("./data/daily_expression_figure2.csv", data.table = FALSE, header = TRUE)

JLshock <- c("PF3D7_0320800", "PF3D7_0410400", "PF3D7_0507600", "PF3D7_0520300", "PF3D7_0720000", "PF3D7_0811300", "PF3D7_0819900", "PF3D7_0909400", "PF3D7_0909900", 
    "PF3D7_1006100", "PF3D7_1032100", "PF3D7_1103800", "PF3D7_1106300", "PF3D7_1107000", "PF3D7_1124400", "PF3D7_1128600", "PF3D7_1209200", "PF3D7_1224300", 
    "PF3D7_1235300", "PF3D7_1307000", "PF3D7_1308900", "PF3D7_1325000", "PF3D7_1340100", "PF3D7_1364500", "PF3D7_1427800", "PF3D7_1443300", "PF3D7_1443500", 
    "PF3D7_1449700", "PF3D7_0519500")

# Load entrex geneID mappings
entrez_geneID_mappings <- fread("./data/geneID_mappings.txt", data.table = FALSE, stringsAsFactors = FALSE)

upcluster2 <- daily_figure2$Gene[daily_figure2$`Up regulated in Cluster 2?` == "Y"]
upcluster1 <- daily_figure2$Gene[daily_figure2$`Up regulated in Cluster 2?` == "N"]
glycolisis <- daily_figure2$Gene[daily_figure2$type == "Glycolisis"]
tricarboxylic <- daily_figure2$Gene[daily_figure2$type == "Tricarboxylic acid cycle"]
fatty_acid <- daily_figure2$Gene[daily_figure2$type == "Fatty acid metabolism"]

upcluster2 <- as.vector(geneID_mappings$current[geneID_mappings$old %in% upcluster2])
upcluster1 <- as.vector(geneID_mappings$current[geneID_mappings$old %in% upcluster1])
glycolisis <- as.vector(geneID_mappings$current[geneID_mappings$old %in% glycolisis])
tricarboxylic <- as.vector(geneID_mappings$current[geneID_mappings$old %in% tricarboxylic])
fatty_acid <- as.vector(geneID_mappings$current[geneID_mappings$old %in% fatty_acid])

indices <- ids2indices(list(up_in_starvation = upcluster1, up_int_vitro = upcluster2, glycolisis = glycolisis, tricarboxylic = tricarboxylic, fatty_acid = fatty_acid, 
    mRNA_degradation = JLshock), rownames(v2$E))
mroast(v2, index = indices, design = modRUV, contrast = 2, nrot = 10000, set.statistic = "floormean")

##                  NGenes  PropDown     PropUp Direction     PValue        FDR PValue.Mixed  FDR.Mixed
## up_int_vitro         12 0.8333333 0.00000000      Down 0.01129887 0.02812219   0.01249875 0.01493851
## glycolisis           19 0.5789474 0.05263158      Down 0.01309869 0.02812219   0.01009899 0.01493851
## mRNA_degradation     29 0.2758621 0.06896552      Down 0.01459854 0.02812219   0.00769923 0.01493851
## tricarboxylic        11 0.1818182 0.36363636        Up 0.01879812 0.02812219   0.00129987 0.00749925
## up_in_starvation     33 0.1818182 0.21212121        Up 0.06249375 0.07493251   0.00929907 0.01493851
## fatty_acid           17 0.1764706 0.11764706        Up 0.12558744 0.12558744   0.07129287 0.07129287

camera(v2, index = indices, design = modRUV, contrast = 2)

##                  NGenes Correlation Direction     PValue       FDR
## up_int_vitro         12  0.52478121      Down 0.08926728 0.3726012
## glycolisis           19  0.21525215      Down 0.12420039 0.3726012
## mRNA_degradation     29  0.05546379      Down 0.23644819 0.4728964
## tricarboxylic        11  0.07171539        Up 0.37832832 0.4837847
## up_in_starvation     33  0.07428553        Up 0.46672227 0.4837847
## fatty_acid           17  0.06532833        Up 0.48378475 0.4837847

System Information

setwd(wd)
sessionInfo()

## R version 3.2.0 (2015-04-16)
## Platform: x86_64-apple-darwin15.4.0 (64-bit)
## Running under: OS X 10.11.6 (unknown)
## 
## locale:
## [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
## 
## attached base packages:
##  [1] grid      stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] pheatmap_1.0.8             knitr_1.15.1               stringr_1.1.0              dplyr_0.5.0                data.table_1.10.0         
##  [6] VennDiagram_1.6.17         futile.logger_1.4.3        RColorBrewer_1.1-2         EDASeq_2.4.1               ShortRead_1.28.0          
## [11] GenomicAlignments_1.6.3    SummarizedExperiment_1.0.2 Rsamtools_1.22.0           GenomicRanges_1.22.4       GenomeInfoDb_1.6.3        
## [16] Biostrings_2.38.4          XVector_0.10.0             IRanges_2.4.8              S4Vectors_0.8.11           BiocParallel_1.4.3        
## [21] Biobase_2.30.0             BiocGenerics_0.16.1        reshape2_1.4.2             ggplot2_2.2.1              ruv_0.9.6                 
## [26] quadprog_1.5-5             edgeR_3.12.1               limma_3.26.9              
## 
## loaded via a namespace (and not attached):
##  [1] splines_3.2.0           R.utils_2.5.0           assertthat_0.1          statmod_1.4.27          highr_0.6               aroma.light_3.0.0      
##  [7] latticeExtra_0.6-28     yaml_2.1.14             RSQLite_1.1-1           backports_1.0.4         lattice_0.20-31         digest_0.6.11          
## [13] colorspace_1.3-2        htmltools_0.3.5         Matrix_1.2-0            R.oo_1.21.0             plyr_1.8.4              XML_3.98-1.5           
## [19] biomaRt_2.26.1          genefilter_1.52.1       zlibbioc_1.16.0         xtable_1.8-2            scales_0.4.1            tibble_1.2             
## [25] annotate_1.48.0         GenomicFeatures_1.22.13 lazyeval_0.2.0          survival_2.40-1         magrittr_1.5            memoise_1.0.0          
## [31] evaluate_0.10           R.methodsS3_1.7.1       hwriter_1.3.2           tools_3.2.0             formatR_1.4             matrixStats_0.51.0     
## [37] munsell_0.4.3           AnnotationDbi_1.32.3    lambda.r_1.1.9          DESeq_1.22.1            RCurl_1.95-4.8          bitops_1.0-6           
## [43] labeling_0.3            rmarkdown_1.3           gtable_0.2.0            DBI_0.5-1               R6_2.2.0                rtracklayer_1.30.4     
## [49] rprojroot_1.1           futile.options_1.0.0    stringi_1.1.2           Rcpp_0.12.8             geneplotter_1.48.0